diff --git a/src/cli/commands/analyze.ts b/src/cli/commands/analyze.ts
index 4f9fcf96..bee57333 100644
--- a/src/cli/commands/analyze.ts
+++ b/src/cli/commands/analyze.ts
@@ -154,8 +154,8 @@ export function registerAnalyze(cli: CAC): void {
         const result = analyzeFile(file, analyzeOptions);
         log(`Nodes: ${result.nodeCount} (max depth: ${result.maxDepth})`);
 
-        // Calculate scores
-        const scores = calculateScores(result);
+        // Calculate scores using the same preset-adjusted configs
+        const scores = calculateScores(result, configs as Record<RuleId, RuleConfig>);
 
         // JSON output mode — only JSON goes to stdout; exit code still applies
         if (options.json) {
diff --git a/src/core/engine/scoring.test.ts b/src/core/engine/scoring.test.ts
index cee9eea2..8b4a792e 100644
--- a/src/core/engine/scoring.test.ts
+++ b/src/core/engine/scoring.test.ts
@@ -87,33 +87,41 @@ describe("calculateScores", () => {
   });
 
   it("uses calculatedScore for density: higher score = more density impact", () => {
-    const heavy = calculateScores(makeResult([
-      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking", score: -10 }),
-    ], 100));
+    // Create issue where calculatedScore differs from config.score
+    const heavyIssue = makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking", score: -10 });
+    heavyIssue.calculatedScore = -15; // Simulate depthWeight effect
 
-    const light = calculateScores(makeResult([
-      makeIssue({ ruleId: "unnecessary-node", category: "structure", severity: "suggestion", score: -2 }),
-    ], 100));
+    const lightIssue = makeIssue({ ruleId: "unnecessary-node", category: "structure", severity: "suggestion", score: -2 });
+    lightIssue.calculatedScore = -2; // No depthWeight
 
+    const heavy = calculateScores(makeResult([heavyIssue], 100));
+    const light = calculateScores(makeResult([lightIssue], 100));
+
+    // Density should use calculatedScore (-15 vs -2), not config.score
+    expect(heavy.byCategory.structure.weightedIssueCount).toBe(15);
+    expect(light.byCategory.structure.weightedIssueCount).toBe(2);
     expect(heavy.byCategory.structure.densityScore).toBeLessThan(
       light.byCategory.structure.densityScore
     );
   });
 
   it("differentiates rules within the same severity by score", () => {
-    const highScore = calculateScores(makeResult([
-      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking", score: -10 }),
-    ], 100));
+    // Create issues where calculatedScore differs from config.score
+    const highScoreIssue = makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking", score: -10 });
+    highScoreIssue.calculatedScore = -15; // Simulate depthWeight effect
 
-    const lowScore = calculateScores(makeResult([
-      makeIssue({ ruleId: "absolute-position-in-auto-layout", category: "structure", severity: "blocking", score: -3 }),
-    ], 100));
+    const lowScoreIssue = makeIssue({ ruleId: "absolute-position-in-auto-layout", category: "structure", severity: "blocking", score: -3 });
+    lowScoreIssue.calculatedScore = -5; // Simulate different depthWeight
+
+    const highScore = calculateScores(makeResult([highScoreIssue], 100));
+    const lowScore = calculateScores(makeResult([lowScoreIssue], 100));
 
+    // weightedIssueCount should use calculatedScore, not config.score
     expect(highScore.byCategory.structure.densityScore).toBeLessThan(
       lowScore.byCategory.structure.densityScore
     );
-    expect(highScore.byCategory.structure.weightedIssueCount).toBe(10);
-    expect(lowScore.byCategory.structure.weightedIssueCount).toBe(3);
+    expect(highScore.byCategory.structure.weightedIssueCount).toBe(15);
+    expect(lowScore.byCategory.structure.weightedIssueCount).toBe(5);
   });
 
   it("density score decreases as weighted issue count increases relative to node count", () => {
@@ -136,15 +144,15 @@ describe("calculateScores", () => {
 
   it("diversity score penalizes more unique rules being triggered", () => {
     const concentrated = calculateScores(makeResult([
-      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk" }),
-      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk" }),
-      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk" }),
+      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk", score: -5 }),
+      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk", score: -5 }),
+      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk", score: -5 }),
     ], 100));
 
     const spread = calculateScores(makeResult([
-      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk" }),
-      makeIssue({ ruleId: "group-usage", category: "structure", severity: "risk" }),
-      makeIssue({ ruleId: "deep-nesting", category: "structure", severity: "risk" }),
+      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "risk", score: -5 }),
+      makeIssue({ ruleId: "group-usage", category: "structure", severity: "risk", score: -5 }),
+      makeIssue({ ruleId: "deep-nesting", category: "structure", severity: "risk", score: -5 }),
     ], 100));
 
     expect(concentrated.byCategory.structure.diversityScore).toBeGreaterThan(
@@ -152,6 +160,39 @@ describe("calculateScores", () => {
     );
   });
 
+  it("diversity weights triggered rules by score severity", () => {
+    // One high-severity rule triggered
+    const heavyRule = calculateScores(makeResult([
+      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking", score: -10 }),
+    ], 100));
+
+    // One low-severity rule triggered
+    const lightRule = calculateScores(makeResult([
+      makeIssue({ ruleId: "unnecessary-node", category: "structure", severity: "suggestion", score: -2 }),
+    ], 100));
+
+    expect(heavyRule.byCategory.structure.diversityScore).toBeLessThan(
+      lightRule.byCategory.structure.diversityScore
+    );
+  });
+
+  it("low-severity rules have minimal diversity impact (intentional)", () => {
+    // 1 suggestion rule (score -2) vs 1 blocking rule (score -10).
+    // Weighted ratio for the suggestion is much smaller, so diversity stays high.
+    // Low-severity rules correctly penalize diversity less.
+    const lowSeverity = calculateScores(makeResult([
+      makeIssue({ ruleId: "unnecessary-node", category: "structure", severity: "suggestion", score: -2 }),
+    ], 100));
+
+    const highSeverity = calculateScores(makeResult([
+      makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking", score: -10 }),
+    ], 100));
+
+    // Both trigger exactly 1 rule, but severity-weighted diversity differs significantly
+    expect(lowSeverity.byCategory.structure.diversityScore).toBeGreaterThan(90);
+    expect(highSeverity.byCategory.structure.diversityScore).toBeLessThan(80);
+  });
+
   it("combined score = density * 0.7 + diversity * 0.3", () => {
     const issues = [
       makeIssue({ ruleId: "no-auto-layout", category: "structure", severity: "blocking" }),
@@ -424,4 +465,4 @@ describe("buildResultJson", () => {
     const withoutKey = buildResultJson("TestFile", result, scores);
     expect(withoutKey.fileKey).toBeUndefined();
   });
-});
+});
\ No newline at end of file
diff --git a/src/core/engine/scoring.ts b/src/core/engine/scoring.ts
index c2c47542..6f8e5bb0 100644
--- a/src/core/engine/scoring.ts
+++ b/src/core/engine/scoring.ts
@@ -1,7 +1,9 @@
 import type { Category } from "../contracts/category.js";
 import { CATEGORIES } from "../contracts/category.js";
+import type { RuleId, RuleConfig } from "../contracts/rule.js";
 import type { Severity } from "../contracts/severity.js";
 import type { AnalysisResult } from "./rule-engine.js";
+import { RULE_CONFIGS, RULE_ID_CATEGORY } from "../rules/rule-config.js";
 import { version as VERSION } from "../../../package.json";
 
 /**
@@ -60,16 +62,27 @@ export type Grade = "S" | "A+" | "A" | "B+" | "B" | "C+" | "C" | "D" | "F";
  */
 
 /**
- * Total rules per category — used as denominator for diversity scoring.
- * Must be updated when rules are added/removed from a category.
+ * Compute sum of |score| for all rules in each category from a given config map.
+ * Used as denominator for severity-weighted diversity scoring.
+ * Must use the same preset-adjusted config map that produced the analysis issues,
+ * otherwise diversity ratios will be incorrect.
  */
-const TOTAL_RULES_PER_CATEGORY: Record<Category, number> = {
-  structure: 9,
-  token: 7,
-  component: 4,
-  naming: 5,
-  behavior: 4,
-};
+function computeTotalScorePerCategory(
+  configs: Record<RuleId, RuleConfig>
+): Record<Category, number> {
+  const totals = Object.fromEntries(
+    CATEGORIES.map(c => [c, 0])
+  ) as Record<Category, number>;
+
+  for (const [id, config] of Object.entries(configs)) {
+    const category = RULE_ID_CATEGORY[id as RuleId];
+    if (category && config.enabled) {
+      totals[category] += Math.abs(config.score);
+    }
+  }
+
+  return totals;
+}
 
 /**
  * Category weights for overall score.
@@ -151,20 +164,35 @@ function clamp(value: number, min: number, max: number): number {
  * Calculate scores from analysis result using density + diversity scoring
  *
  * Density Score = 100 - (weighted issue count / node count) * 100
- * Diversity Score = (1 - unique rules / total category rules) * 100
+ * Diversity Score = (1 - weighted triggered rule scores / total category scores) * 100
  * Final Score = density * 0.7 + diversity * 0.3
+ *
+ * @param result Analysis result with issues
+ * @param configs Optional preset-adjusted config map used to produce the issues.
+ *                If not provided, diversity totals are reconstructed from issue.config values.
  */
-export function calculateScores(result: AnalysisResult): ScoreReport {
+export function calculateScores(
+  result: AnalysisResult,
+  configs?: Record<RuleId, RuleConfig>
+): ScoreReport {
   const categoryScores = initializeCategoryScores();
   const nodeCount = result.nodeCount;
 
-  // Track unique rules per category
+  // Track unique rules and their base |score| per category
   const uniqueRulesPerCategory = new Map<Category, Set<string>>();
+  const ruleScorePerCategory = new Map<Category, Map<string, number>>();
   for (const category of CATEGORIES) {
     uniqueRulesPerCategory.set(category, new Set());
+    ruleScorePerCategory.set(category, new Map());
   }
 
-  // Count issues by severity per category and track unique rules
+  // Compute totals from the config map.
+  // If configs provided: use preset-adjusted totals (recommended when using presets).
+  // If not: fall back to static RULE_CONFIGS — only correct when issues were
+  // produced with default RULE_CONFIGS, otherwise diversity ratios will be skewed.
+  const totalScorePerCategory = computeTotalScorePerCategory(configs ?? RULE_CONFIGS);
+
+  // Count issues by severity per category and track unique rules with scores
   for (const issue of result.issues) {
     const category = issue.rule.definition.category;
     const severity = issue.config.severity;
@@ -174,13 +202,13 @@ export function calculateScores(result: AnalysisResult): ScoreReport {
     categoryScores[category].bySeverity[severity]++;
     categoryScores[category].weightedIssueCount += Math.abs(issue.calculatedScore);
     uniqueRulesPerCategory.get(category)!.add(ruleId);
+    ruleScorePerCategory.get(category)!.set(ruleId, Math.abs(issue.config.score));
   }
 
   // Calculate percentage for each category based on density + diversity
   for (const category of CATEGORIES) {
     const catScore = categoryScores[category];
     const uniqueRules = uniqueRulesPerCategory.get(category)!;
-    const totalRules = TOTAL_RULES_PER_CATEGORY[category];
 
     catScore.uniqueRuleCount = uniqueRules.size;
 
@@ -192,11 +220,17 @@ export function calculateScores(result: AnalysisResult): ScoreReport {
     }
     catScore.densityScore = densityScore;
 
-    // Diversity score: fewer unique rules = higher score (issues are concentrated)
-    // If no issues, diversity score is 100 (perfect)
+    // Diversity score: weighted by base rule |score| (config.score, not calculatedScore).
+    // Uses base score intentionally — diversity measures "what types of problems exist",
+    // not "where they occur". depthWeight affects density (volume penalty) but not diversity
+    // (breadth penalty). A blocking rule (score -10) penalizes diversity more than a
+    // suggestion (score -1), so low-severity-only designs correctly get high diversity scores.
     let diversityScore = 100;
     if (catScore.issueCount > 0) {
-      const diversityRatio = uniqueRules.size / totalRules;
+      const ruleScores = ruleScorePerCategory.get(category)!;
+      const weightedTriggered = Array.from(ruleScores.values()).reduce((sum, s) => sum + s, 0);
+      const weightedTotal = totalScorePerCategory[category];
+      const diversityRatio = weightedTotal > 0 ? weightedTriggered / weightedTotal : 0;
       diversityScore = clamp(Math.round((1 - diversityRatio) * 100), 0, 100);
     }
     catScore.diversityScore = diversityScore;
@@ -392,4 +426,4 @@ export function buildResultJson(
   }
 
   return json;
-}
+}
\ No newline at end of file
diff --git a/src/core/rules/rule-config.ts b/src/core/rules/rule-config.ts
index a60aaa27..0018ef7a 100644
--- a/src/core/rules/rule-config.ts
+++ b/src/core/rules/rule-config.ts
@@ -1,5 +1,42 @@
+import type { Category } from "../contracts/category.js";
 import type { RuleConfig, RuleId } from "../contracts/rule.js";
 
+/**
+ * Maps each rule ID to its category. Kept alongside RULE_CONFIGS so both
+ * are updated together when rules are added or removed.
+ */
+export const RULE_ID_CATEGORY: Record<RuleId, Category> = {
+  "no-auto-layout": "structure",
+  "absolute-position-in-auto-layout": "structure",
+  "fixed-size-in-auto-layout": "structure",
+  "missing-size-constraint": "structure",
+  "missing-responsive-behavior": "structure",
+  "group-usage": "structure",
+  "deep-nesting": "structure",
+  "z-index-dependent-layout": "structure",
+  "unnecessary-node": "structure",
+  "raw-color": "token",
+  "raw-font": "token",
+  "inconsistent-spacing": "token",
+  "magic-number-spacing": "token",
+  "raw-shadow": "token",
+  "raw-opacity": "token",
+  "multiple-fill-colors": "token",
+  "missing-component": "component",
+  "detached-instance": "component",
+  "missing-component-description": "component",
+  "variant-structure-mismatch": "component",
+  "default-name": "naming",
+  "non-semantic-name": "naming",
+  "inconsistent-naming-convention": "naming",
+  "numeric-suffix-name": "naming",
+  "too-long-name": "naming",
+  "text-truncation-unhandled": "behavior",
+  "prototype-link-in-design": "behavior",
+  "overflow-behavior-unknown": "behavior",
+  "wrap-behavior-unknown": "behavior",
+};
+
 /**
  * Central configuration for all rules
  * Edit scores/severity here without touching rule logic
diff --git a/src/mcp/server.ts b/src/mcp/server.ts
index bb42b053..e19dc16d 100644
--- a/src/mcp/server.ts
+++ b/src/mcp/server.ts
@@ -123,7 +123,7 @@ IMPORTANT — Before calling this tool, check which data source is available:
         ...(effectiveNodeId ? { targetNodeId: effectiveNodeId } : {}),
       });
 
-      const scores = calculateScores(result);
+      const scores = calculateScores(result, configs as Record<RuleId, RuleConfig>);
 
       // Generate HTML report (with Figma token for comment buttons)
       const figmaToken = token ?? process.env["FIGMA_TOKEN"];