Here’s a simple test I performed with GD waaaaay back when the Deck was first announced…
Set the game to the Deck’s resolution. Make sure the non-Steam controller option in the Keybinding settings is toggled on if not using a Steam controller.
Enter the game. Report back exactly what occurs at this juncture.
Bonus points:
If you really want to replicate it a little more then install something like Manjaro Linux (which is Arch-based, just like SteamOS 3) and test the above there as well.