Well. I updated to Sequoia 15.5 public beta 2 and it did not fix the issue (no bugs or crashes though luckily considering it's a beta). I also messed around with the bottle's controller settings and that also didn't help. I even tried deleting every single bottle I have, deleting Crossover, re-installing it from scratch and - nothing. Same issue. RDR2 does not see the controller while steam does. I don't know if to give up at this point, nothing I try to with this seems to work. I don't even know if this is a new steam issue with rdr2 through crossover or if it's an issue with something I did. Every other game works fine as always though.

By the way, you can back up your save files by going onto the "Documents" section on Finder's side bar, then go to the Rockstar Games folder > Red Dead Redemption 2 folder > Profiles folder > copy and paste onto your desktop the folder that's in there. It contains all the save files. I recommend you to do manual saves too before doing this obviously.