After talking to my friends at Apple, the advice I got is to use the same bundle ID both on and outside the Mac App Store, and to file Radar bug reports about the problems with doing so. This is a change from the consensus I found yesterday, but it’s unofficially from an official source, so I’m considering it gospel.
Separately, I see that some developers decided to go exclusively Mac App Store: Pixelmator, TapeDeck, and Coversutra are all only in the MAS. But I also see a lot of customer backlash to that, so for me that’s not a solution.