Problem/Motivation
We already inject Composer's autoloader into DrupalKernel, yet drupal_classloader() creates its own classloader with a hardcoded reference to Drupal's core/vendor/autolod.php. Therefore it is not possible to use a different autoloader simply by passing a different one into DrupalKernel.
Proposed resolution
Always use DrupalKernel's autoloader. For this purpose a getClassLoader() method is introduced on DrupalKernelInterface. This is consumed by drupal_classloader_register(). Alternatively, drupal_classloader_register() could be replaced directly by a new method on the kernel or the already existing classloaderAddMultiplePsr4(). In order to still support ApcClassLoader for PHP 5.3 a setClassLoader() method is introduced. This is (optionally) being called from index.php directly now.
With these changes Drupal can be run with a completely custom classloader (as long as that classloader contains the right classes, obviously).