Update: the official word is to use the same bundle ID. See here.
If you use the same bundle ID for both the MAS (Mac App Store) and non-MAS versions of your app, you have one set of issues to deal with. If the same or newer version of the app exists on the computer, the customer can’t buy the MAS version, nor can they rate or review the app, even if they bought it outside the MAS.
If you use a different bundle ID for the two versions, you have another set of issues. The system will treat the two version as completely different apps, even though they have identical functionality and name. The customer who already bought your app might end up buying it a second time in the MAS.
It’s a dilemma because neither of the choices are good choices. Daniel Jalkut filed two Radar bug reports with Apple, one for using the same bundle ID and one for using a different bundle ID.
Earlier I was sure I had to use a different bundle ID, but now I’m not so sure.