I am using proton to play on linux. I had an issue where I only saw the controller interface (Buttons A, B, X and Y) instead of the according computer keyboard key binds. I was wondering why and I found the solution, that turning off the "xboxdrv.service" using:
systemctl stop xboxdrv.service
and then starting the game fixed that issue since it does no longer think that I am playing on console. Maybe this is helpful for you or anyone reads this in the future.