I'm not sure I can detect whether another app is non-natively full screened, I'm afraid. I'll give it a poke, but to be honest, working with full screen stuff is a bit difficulty on OS X. The APIs aren't super comprehensive.
Filling up rather than emptying out is a fun idea; I'll add that to the ol' feature request list.
- Spotlight searches makes it flicker
- Make it narrow for non-native (i.e. not only lion style) full screen aswell. It's awfully disturbing together with full screen iTerm, MacVim etc.
Other than that it's quite neat! I'd rather have it fill than empty though, maybe make that an option? ;)