Load the autoloader as soon as the Drupal root is identified.

includes/drupal.inc

@@ -13,14 +13,17 @@ use Drush\Drush;
 function drush_drupal_load_autoloader($drupal_root) {
   static $autoloader = FALSE;
 
-  if (!$autoloader) {
-    $autoloader = require $drupal_root .'/autoload.php';
-    if ($autoloader === TRUE) {
-      // The autoloader was already require(). Assume that Drush and Drupal share an autoloader per
-      // "Point autoload.php to the proper vendor directory" - https://www.drupal.org/node/2404989
-      $autoloader = drush_get_context('DRUSH_CLASSLOADER');
-    }
+  $autoloadFilePath = $drupal_root .'/autoload.php';
+  if (!$autoloader && file_exists($autoloadFilePath)) {
+    $autoloader = require $autoloadFilePath;
+  }
+
+  if ($autoloader === TRUE) {
+    // The autoloader was already requireed. Assume that Drush and Drupal share an autoloader per
+    // "Point autoload.php to the proper vendor directory" - https://www.drupal.org/node/2404989
+    $autoloader = drush_get_context('DRUSH_CLASSLOADER');
   }
+
   return $autoloader;
 }
 

includes/preflight.inc

@@ -497,19 +497,9 @@ function drush_preflight() {
   drush_preflight_site();
 
   // Check to see if anything changed during the 'site' preflight
-  // that might allow us to find our alias record now
+  // that might allow us to find our alias record now.
   if (empty($alias_record)) {
     $alias_record = _drush_sitealias_set_context_by_name($target_alias);
-
-    // If the site alias settings changed late in the preflight,
-    // then run the preflight for the root and site contexts again.
-    if (!empty($alias_record)) {
-      $remote_host = drush_get_option('remote-host');
-      if (!isset($remote_host)) {
-        drush_preflight_root();
-        drush_preflight_site();
-      }
-    }
   }
 
   // Fail if we could not find the selected site alias.
@@ -544,6 +534,9 @@ function drush_preflight() {
 function drush_preflight_root() {
   $root = drush_get_option('root');
   Drush::bootstrapManager()->locateRoot($root);
+  // Load the autoload file and provide it to the bootstrap manager.
+  $siteAutoloader = drush_drupal_load_autoloader($root);
+  Drush::bootstrapManager()->setAutoloader($siteAutoloader);
 
   // Load the config options from Drupal's /drush, ../drush, and sites/all/drush directories,
   // even prior to bootstrapping the root.

includes/sitealias.inc

@@ -1772,8 +1772,6 @@ function _drush_sitealias_set_context_by_name($alias, $prefix = '') {
         }
 
         _drush_sitealias_cache_alias('@self', $site_alias_settings);
-        // Change the selected site to match the new --root and --uri, if any were set.
-        _drush_preflight_root_uri();
       }
       return $site_alias_settings;
     }

src/Boot/AutoloaderAwareInterface.php

@@ -0,0 +1,11 @@
+<?php
+namespace Drush\Boot;
+
+interface AutoloaderAwareInterface
+{
+    public function setAutoloader($loader);
+
+    public function autoloader();
+
+    public function hasAutoloader();
+}

src/Boot/AutoloaderAwareTrait.php

@@ -0,0 +1,22 @@
+<?php
+namespace Drush\Boot;
+
+trait AutoloaderAwareTrait
+{
+    protected $loader;
+
+    public function setAutoloader($loader)
+    {
+        $this->loader = $loader;
+    }
+
+    public function autoloader()
+    {
+        return $this->loader;
+    }
+
+    public function hasAutoloader()
+    {
+        return false;
+    }
+}

src/Boot/BootstrapManager.php

@@ -8,9 +8,10 @@
 use Psr\Log\LoggerAwareInterface;
 use Psr\Log\LoggerAwareTrait;
 
-class BootstrapManager implements LoggerAwareInterface
+class BootstrapManager implements LoggerAwareInterface, AutoloaderAwareInterface
 {
     use LoggerAwareTrait;
+    use AutoloaderAwareTrait;
 
     /**
      * @var DrupalFinder
@@ -137,6 +138,9 @@ public function bootstrapObjectForRoot($path)
     {
         foreach ($this->bootstrapCandidates as $candidate) {
             if ($candidate->validRoot($path)) {
+                if ($candidate instanceof AutoloaderAwareInterface) {
+                    $candidate->setAutoloader($this->autoloader());
+                }
                 return $candidate;
             }
         }

src/Boot/DrupalBoot8.php

@@ -11,8 +11,9 @@
 
 use Drush\Log\LogLevel;
 
-class DrupalBoot8 extends DrupalBoot
+class DrupalBoot8 extends DrupalBoot implements AutoloaderAwareInterface
 {
+    use AutoloaderAwareTrait;
 
       /**
        * @var \Drupal\Core\DrupalKernelInterface
@@ -40,8 +41,10 @@ public function validRoot($path)
 
     public function getVersion($drupal_root)
     {
-        // Load the autoloader so we can access the class constants.
-        drush_drupal_load_autoloader($drupal_root);
+        // Are the class constants available?
+        if (!$this->hasAutoloader()) {
+            throw new \Exception('Cannot access Drupal 8 class constants - Drupal autoloader not loaded yet.');
+        }
         // Drush depends on bootstrap being loaded at this point.
         require_once $drupal_root .'/core/includes/bootstrap.inc';
         if (defined('\Drupal::VERSION')) {
@@ -129,7 +132,7 @@ public function bootstrapDrupalDatabase()
     public function bootstrapDrupalConfiguration()
     {
         $this->request = Request::createFromGlobals();
-        $classloader = drush_drupal_load_autoloader(DRUPAL_ROOT);
+        $classloader = $this->autoloader();
         // @todo - use Request::create() and then no need to set PHP superglobals
         $kernelClass = new \ReflectionClass('\Drupal\Core\DrupalKernel');
         if ($kernelClass->hasMethod('addServiceModifier')) {