I finally decided how to deal with Basculin in my patch. When any Basculin is generated (both wild and trainer), a random calculation is run, which chooses which form of Basculin you will see.
I decided to do this because I can't have a "White" or a "Black" Basculin, which only appears on one specific ROM. However, I can provide a way which will only allow one or the other to be generated. The important thing here is that it wouldn't prevent the "other" Basculin from being able to appear in the ROM in question through a link battle or a trade.
To ensure only one Basculin form appears in your ROM, navigate to 0x7669F8 and change it to:
087669F8: XX 20
087669FA: 00 00
Where the XX is:
00 - Red Striped Basculin
01 - Blue Striped Basculin
ETA: I extended this functionality to set any Burmy found (either in the wild or in a trainerbattle) automatically to the correct cloak. You still can't switch between them at will, but at least if you're in a cave or on a beach, the game will correctly generate a Sandy Cloaked Burmy, or if you're in a house or "No environment" (I'm honestly not sure what that means), it'll generate a Trash Cloaked Burmy.
I will also add this info to the first post so it doesn't get lost to the mists of time.