Bootstrap messes up with default theme registry and template engines

Commit causing this issue

Using a git bisect, this regression has been introduced with #2223885: Detect standalone hook_[pre]process_THEME_HOOK__SUGGESTION implementations

Pre-requisites to reproduce

Use another theme engine such as Twig (https://www.drupal.org/project/tfd7), to install, follow instruction at http://makina-corpus.com/blog/metier/2015/howto-using-twig-in-drupal-7

Especially the part stating that bootstrap should be using the same theme engine due to a core bug:

/**
 * Implements hook_system_info_alter().
 */
function mymodule_system_info_alter(&$info, $file, $type) {
  // Tweak bootstrap so it would be considered as a twig-based theme.
  if ($type == 'theme' && $info['name'] == 'Bootstrap') {
    $info['engine'] = 'twig';
  }
}

The problem

Before this commit, the default templates (node.tpl.php, region.tpl.php) provided by their respective modules are picked up if they are not defined in your own theme, nor in bootstrap, meaning you have to override each template bootstrap was providing in your theme, hence this gist https://gist.github.com/SebCorbin/2297f50b79d1c676eb04

But after this commit, Drupal is looking for modules/system/region.tpl.twig instead of picking the default region.tpl.php.

Then I noted that all system templates are overriden in bootstrap. It seems you have put a huge amount of work in this and I don't know how to fix the usage of different template engines.
I can help provide a patch but would you prefer we try to fix this, or a workaround to deactivate this part of the code which rewrites the whole registry but breaks some concepts?