theme initialized before hook_custom_theme is called.

#2069023: Fix reaction to disabled modules introduced search_api_system_info_alter().
Because of a call to l() it can make drupal_theme_initialize() run too early in the progress (before the full bootrap).
The hook is in my case invoked by features, but since side-wide content is generated with a theme specific function I think this is a bug in search_api.

Stripped version of the debug backtrace:

menu_get_custom_theme() <-- $initialize is FALSE by default, so this function will return NULL
drupal_theme_initialize()
l()
search_api_system_info_alter()
...
system_rebuild_module_data()
features_get_info()
...
feature_load()
...
drupal_path_initialize()
_drupal_bootstrap_full()
...

I attached a patch that fixes the problem for me. My proposed solution is to solve this the same way as usually done in hook_requirements() where the link is not created with l(), but by creating the a element directly.
I tried to create a test to reproduce the problem, but could not get it working. It looks like there is some other variable like a hook_preprocess_link() or something that is defined in one of the other modules I have enabled, and is not enabled on a clean testing environment.