Will Game Boy Advance be selected as a different console or is it two different

I've never personally played the gba one but based off of video footage I've seen, I'm going to say it's probably a separate game. It looks like there is currently not a GBA version of this game on speedrun.com. so if you really want to run the GBA version, i would suggest making a submission to speedrun.com

The GBA version of the game is an entirely different game that shares pretty much none of the mechanics from what I understand. If you have interest in running the GBA game, I believe you'd need to make a page for that yourself (like I did for this game)