I know there are a few cases, like having to check when the bank is opened on addon load, but they're few and far between. The mass majority of addons, if coded to use the proper init events, can be made LoD with a quick change in the TOC.
GC can fire during load, many times actually, and that's NORMAL (you load shit, it hits the threshold, GC triggers, the threshold raises, load more shit...). Due to the new GC system we got with, what, WoW 2.0? ... this really shouldn't matter anyway, they're GC steps, not full blown GCs.
I was talking about reducing or eliminating version conflicts with Libs.
You don't understand how embedded libs work :P If everything you run is using release versions of libs (like they should be), then you should never run into any conflicts unless someone releases a lib that has a conflict (which they shouldn't be if they're testing things out before release)