That's funny. When I tried to alter my MAS version of KOTOR with the widescreen hack, it would no longer launch. And when I tried to make some changes to my copy of Avernum 6 so I could see secret doors more clearly, it would no longer launch. I would say my point is quite valid.
Now, whether the new version of BG handles mods in such a way that the core executable is not altered remains to be seen. But all Mac App Store applications contain a checksum that must exactly match the app being launched. It has something to do with Apple trying to protect us from malware or viruses or something, but it just lowers the value of the software we buy, in my opinion.