This is a bad idea on so many levels. You should always talk to the most specific version of your settings rather than have the super generic one try to add extra stuff from another module that it loaded.
Sorry, I'm not getting it... but I'd love some elaboration on where this causes problems. It's also worth mentioning (you'll note the if DEBUG bit) that this is only something we use locally to make it easy to toss stuff like the debug toolbar in, etc.