This might be late but if you’re using lutris from flatpak you need to run a command to allow lutris to have access to the gamepad.
The command is
flatpak --user override --filesystem=/run/udev:ro net.lutris.Lutris
Source: https://www.reddit.com/r/SteamDeck/comments/x6i9zo
Really late for an answer. I was already using flatseal for some flatpack permission. Use it to add the folder in the command line, and the controller seem to work correctly. Thanks!