G/S/C (and HG/SS, and fan remakes) make use of alternate battle music (wild Pokémon, trainer, and gym leader) depending on if the player is in Johto or Kanto. From what I understand, the current hacks out there do this by having the game store tracks in variables and switching them out whenever the player switches regions through one of a very limited amount of means. Such code would directly conflict with the GB Player code, making it impossible to have both without making things awfully convoluted.
It's a shame, really. But I guess that's what HG/SS are for. If anything, someone needs to get to improving the quality of the 8-bit music in those games!