Move the alternative layout functionality out of the theme layer

Sadly, I can't make this work in the theme layer. I tried many different approaches (some of which were extremely interesting/cool [but potentially hacky]) but couldn't come up with a solution that fixes ALL of the existing problems. I now reached a point where the layout functionality works flawlessly on the theme layer except for one situation: When you clear the cache on the backend (as in... clear the cache on a page that is _not_ an Omega subtheme) the Omega alter hook for injecting the regions of an alternative layout is never invoked because drupal_alter() only hits the active theme and it's base themes. I found a way to still make this work on the front-end by executing another re-build once we hit the front-end BUT... if you visit a page like /admin/structure/blocks (which requires that information but is also on the backend) I have no way to fix it in time for the page to show the proper regions. This is a major problem and I have yet to find a solution... But it seems as if we have to move this functionality over to the theme layer...