There's a shop in a Zelda game that's only accessible if you put your Game Boy Color cartridge into a Game Boy Advance. MarkDarkness believes that the GBC BIOS could be slightly different on a GBA.
That cartridge is not a GBA title, though. It's a GBC one.
Shantae has also a GBA exclusive transformation.
I didn't actually know that
Are you sure its not the reverse Nebuleon? Instead of a slightly modded bios with a GBA flag of some sort, that the game itself checks for GBA Hardware or serial?
Like
Check Hardware= CGB-001 Run GBC Mode
or
Check Hardware= AGB-001 Run GBA Mode
Though I would more suspect it would check for the presence of the AGP CPU