Hmm... Would Perian conflict with already installed DivX codecs and/or Flip4Mac plugins? Would QT simply choose one based on its capabilities or rather based on which one comes first alphanumerically?
If past experience with Divx and 3ivx is any indication...it's kind of arbitrary. It's certainly not alphanumeric, since some versions of Divx took priority over 3ivx and some did not. It might have something to do with versions numbers or bundle identifiers, but it seems pretty random to me. But the important thing is that it's always consistent; if QT uses one over another once, you can be sure it'll always do so (at least until you install a different version of one).
I can tell you from my own tests that with both Divx and Perian installed, I can open Divx-based AVIs that the Divx codec could not handle, so Perian must be handling AVI parsing. However, judging by QuickTime Player's movie info, the Divx codec is still the doing the actual video decoding. So they each take priority for one task, I guess, for some mystical reason.
That said, I'm not sure there's any reason to keep Divx installed with Perian, since Perian does it all. Perian has no encoder, but luckily Divx is split into two components, so you can just remove its decoder and leave its encoder.
Of course, I've only been using Perian for a few days since I heard about it on this forum. Could be there are gotchas I just haven't encountered yet.