Back in high school when I had lesser moral values in regards to piracy I used a Game Boy emulator that let you pick what mode to play games in. You could select original Game Boy, Super Game Boy or Game Boy Color (GBA had not yet been released). It was great because obviously a game like Donkey Kong was better played in SGB mode while Link's Awakening DX would be ideal in GBC mode. If Nintendo offered that, it would solve any Advance Store issues. If you can pick GB, SGB, GBC or GBA then it all falls on the player and Nintendo does not have to think about what presentation best suits each game.
I fully expect the Advance Store to not be available because I just don't think Nintendo will think about it. Odds are they just hand this sort of thing off to some intern who wouldn't even necessarily know that there is any GBA exclusive feature and would just logically think that a GBC game should use a GBC emulator. If you don't know ahead of time you wouldn't even think to look.