diff --git a/.github/scripts/__tests__/agents-pr-meta-update-body.test.js b/.github/scripts/__tests__/agents-pr-meta-update-body.test.js
index be674acb6..1fca90926 100644
--- a/.github/scripts/__tests__/agents-pr-meta-update-body.test.js
+++ b/.github/scripts/__tests__/agents-pr-meta-update-body.test.js
@@ -446,6 +446,20 @@ test('buildSourceContextResolvedCommentBody explains sync-campaign source contex
   assert.ok(result.includes('No linked GitHub issue is required'));
 });
 
+test('buildSourceContextResolvedCommentBody explains issue-backed source context', () => {
+  const result = buildSourceContextResolvedCommentBody(123, {
+    sourceType: 'github_issue',
+    issueNumber: 456,
+    sourceRef: '#456',
+    requiresIssue: true,
+  });
+
+  assert.ok(result.includes('origin=github_issue'));
+  assert.ok(result.includes('ref=#456'));
+  assert.ok(result.includes('A linked GitHub issue is present'));
+  assert.ok(!result.includes('No linked GitHub issue is required'));
+});
+
 test('resolveExplicitNonIssueWorkflowSourceContext preserves explicit automation source despite stale issue preamble', () => {
   const context = resolveExplicitNonIssueWorkflowSourceContext({
     body: [
@@ -487,11 +501,11 @@ test('resolveExplicitNonIssueWorkflowSourceContext ignores source issue markers'
   assert.equal(context, null);
 });
 
-test('resolveNonIssueWorkflowSourceContextForBodySync preserves issue-sourced sync precedence', () => {
+test('resolveNonIssueWorkflowSourceContextForBodySync preserves explicit issue-sourced sync precedence', () => {
   const context = resolveNonIssueWorkflowSourceContextForBodySync(
     {
       body: [
-        '<!-- meta:issue:123 -->',
+        'Closes #123',
         '<!-- workflow-source:local_request -->',
         '<!-- workflow-source-ref:codex-thread-2026-04-26 -->',
       ].join('\n'),
@@ -502,6 +516,22 @@ test('resolveNonIssueWorkflowSourceContextForBodySync preserves issue-sourced sy
   assert.equal(context, null);
 });
 
+test('resolveNonIssueWorkflowSourceContextForBodySync lets explicit non-issue markers replace generated issue metadata', () => {
+  const context = resolveNonIssueWorkflowSourceContextForBodySync(
+    {
+      body: [
+        '<!-- meta:issue:123 -->',
+        '<!-- workflow-source:local_request -->',
+        '<!-- workflow-source-ref:codex-thread-2026-04-26 -->',
+      ].join('\n'),
+    },
+    123,
+  );
+
+  assert.equal(context.sourceType, 'local_request');
+  assert.equal(context.sourceRef, 'codex-thread-2026-04-26');
+});
+
 test('hasExplicitIssueSyncReference ignores heuristic issue-number sources', () => {
   assert.equal(
     hasExplicitIssueSyncReference({
@@ -512,7 +542,13 @@ test('hasExplicitIssueSyncReference ignores heuristic issue-number sources', ()
     false,
   );
   assert.equal(hasExplicitIssueSyncReference({ body: 'Closes #123' }), true);
-  assert.equal(hasExplicitIssueSyncReference({ body: '<!-- meta:issue:123 -->' }), true);
+  assert.equal(hasExplicitIssueSyncReference({ body: 'Related to #123' }), true);
+  assert.equal(hasExplicitIssueSyncReference({ body: 'Related to issue #123' }), true);
+  assert.equal(hasExplicitIssueSyncReference({ body: 'References issue #123' }), true);
+  assert.equal(hasExplicitIssueSyncReference({ body: 'source issue #123' }), true);
+  assert.equal(hasExplicitIssueSyncReference({ body: 'This issue only mentions review follow-up PR #123' }), false);
+  assert.equal(hasExplicitIssueSyncReference({ body: 'refs in this paragraph mention PR #123' }), false);
+  assert.equal(hasExplicitIssueSyncReference({ body: '<!-- meta:issue:123 -->' }), false);
 });
 
 test('resolveNonIssueWorkflowSourceContextForBodySync honors explicit non-issue markers over heuristics', () => {
diff --git a/.github/scripts/agents_pr_meta_update_body.js b/.github/scripts/agents_pr_meta_update_body.js
index 9c0969b1c..a65589cb0 100644
--- a/.github/scripts/agents_pr_meta_update_body.js
+++ b/.github/scripts/agents_pr_meta_update_body.js
@@ -980,13 +980,16 @@ async function createIssueCommentWithRetry({ github, owner, repo, issueNumber, b
 }
 
 function buildSourceContextResolvedCommentBody(prNumber, sourceContext) {
+  const isIssueBacked = sourceContext?.requiresIssue || sourceContext?.issueNumber || sourceContext?.sourceType === SOURCE_TYPES.GITHUB_ISSUE;
   return [
     '<!-- missing-issue-warning -->',
     '### Workflow source detected',
     '',
     `PR #${prNumber} now has valid workflow source context (${formatSourceContextForLog(sourceContext)}).`,
     '',
-    'No linked GitHub issue is required for this PR.',
+    isIssueBacked
+      ? 'A linked GitHub issue is present for this PR.'
+      : 'No linked GitHub issue is required for this PR.',
   ].join('\n');
 }
 
@@ -1024,13 +1027,10 @@ function resolveExplicitNonIssueWorkflowSourceContext(pr = {}) {
 }
 
 function hasExplicitIssueSyncReference(pr = {}) {
-  const body = String(pr.body || '');
-  if (/<!--\s*meta:issue:[0-9]+\s*-->/i.test(body)) {
-    return true;
-  }
-
-  const text = `${pr.title || ''}\n${body}`;
-  return /\b(?:close[sd]?|closing|fix(?:e[sd])?|fixing|resolve[sd]?|resolving|address(?:e[sd])?|addressing|relate[sd]?\s+to|refs?|references?|issue|source\s+issue|github\s+issue)\s*[:#-]?\s*#[0-9]+\b/i.test(text);
+  const text = `${pr.title || ''}\n${pr.body || ''}`;
+  const explicitClosingReference = /\b(?:close[sd]?|closing|fix(?:e[sd])?|fixing|resolve[sd]?|resolving|address(?:e[sd])?|addressing)\s*[:#-]?\s*#[0-9]+\b/i;
+  const explicitIssueReference = /\b(?:(?:relate[sd]?\s+to|references?)\s+(?:issue\s+)?|(?:source|github|linked)\s+issue\s*)[:#-]?\s*#[0-9]+\b/i;
+  return explicitClosingReference.test(text) || explicitIssueReference.test(text);
 }
 
 function resolveNonIssueWorkflowSourceContextForBodySync(pr = {}, issueNumber = null) {
diff --git a/templates/consumer-repo/.github/scripts/agents_pr_meta_update_body.js b/templates/consumer-repo/.github/scripts/agents_pr_meta_update_body.js
index 9c0969b1c..a65589cb0 100644
--- a/templates/consumer-repo/.github/scripts/agents_pr_meta_update_body.js
+++ b/templates/consumer-repo/.github/scripts/agents_pr_meta_update_body.js
@@ -980,13 +980,16 @@ async function createIssueCommentWithRetry({ github, owner, repo, issueNumber, b
 }
 
 function buildSourceContextResolvedCommentBody(prNumber, sourceContext) {
+  const isIssueBacked = sourceContext?.requiresIssue || sourceContext?.issueNumber || sourceContext?.sourceType === SOURCE_TYPES.GITHUB_ISSUE;
   return [
     '<!-- missing-issue-warning -->',
     '### Workflow source detected',
     '',
     `PR #${prNumber} now has valid workflow source context (${formatSourceContextForLog(sourceContext)}).`,
     '',
-    'No linked GitHub issue is required for this PR.',
+    isIssueBacked
+      ? 'A linked GitHub issue is present for this PR.'
+      : 'No linked GitHub issue is required for this PR.',
   ].join('\n');
 }
 
@@ -1024,13 +1027,10 @@ function resolveExplicitNonIssueWorkflowSourceContext(pr = {}) {
 }
 
 function hasExplicitIssueSyncReference(pr = {}) {
-  const body = String(pr.body || '');
-  if (/<!--\s*meta:issue:[0-9]+\s*-->/i.test(body)) {
-    return true;
-  }
-
-  const text = `${pr.title || ''}\n${body}`;
-  return /\b(?:close[sd]?|closing|fix(?:e[sd])?|fixing|resolve[sd]?|resolving|address(?:e[sd])?|addressing|relate[sd]?\s+to|refs?|references?|issue|source\s+issue|github\s+issue)\s*[:#-]?\s*#[0-9]+\b/i.test(text);
+  const text = `${pr.title || ''}\n${pr.body || ''}`;
+  const explicitClosingReference = /\b(?:close[sd]?|closing|fix(?:e[sd])?|fixing|resolve[sd]?|resolving|address(?:e[sd])?|addressing)\s*[:#-]?\s*#[0-9]+\b/i;
+  const explicitIssueReference = /\b(?:(?:relate[sd]?\s+to|references?)\s+(?:issue\s+)?|(?:source|github|linked)\s+issue\s*)[:#-]?\s*#[0-9]+\b/i;
+  return explicitClosingReference.test(text) || explicitIssueReference.test(text);
 }
 
 function resolveNonIssueWorkflowSourceContextForBodySync(pr = {}, issueNumber = null) {