Switch 2 pro-controller in handheld issue

I'll start by saying this game is amazing, been totally sleeping on it.

I'm having a very specific issue of trying to use an external controller on my Switch 2 in handheld mode. It sets the controller to #2 and forces me to use the joycons. Even if I re-pair the controllers in the menu, when I launch the game it turns off my pro controller and goes back to joycons.

Does anyone know if there's a fix for this? I play a lot on my desk this way and the joycons are not very comfortable for long term play.