Happy to see. I tried playing the Linux version of PokeMMO and it sees "Steam Controller" and adds it in the game settings, but I cannot remap any of the controls. Even adding the game to Steam as a non-Steam game won't work as Steam Input/Overlay can't wrap around the process correctly(or at least I couldn't find a way).

Ended up downloading the .exe version, added that to Steam, and then I could use Steam Input to play the game and setup controller layouts for it.