You recently updated the Steam version of the game to fix problems with running it on the Steam Deck. However, this update is not on the GOG or Itch.io versions (and yes, you can play GOG/itch games on the Steam Deck, so that's not an excuse).

I doubt that they look the GOG forums. You should probably contact them through here.Just Scroll down choose PC and Crosscode and let them know to update the Linux build of crosscode with the new steam deck update for the GOG version.
https://www.deck13.com/contact/support/

I agree, they need to update this GOG version.

However, you can get it running properly on the steam deck if you feel like messing around with it.
There's a discussion in the steam forum that goes over it. I was able to get my copy to work on the steam deck following it.

https://steamcommunity.com/app/368340/discussions/0/3272436223684818200/

Basically....

CossCode (GOG)
-Use linux install version
-Trigger buttons will not work with this install unless the below is done:
-Download https://dl.nwjs.io/v0.63.0/nwjs-v0.63.0-linux-x64.tar.gz
-Replace files in Crosscode with above
-Rename new nw executable to CrossCode
-Start game with start.sh in primary directory