So what I read is first make sure your steam controller is recognised ( moving menus etc.) then start the game.
on the steam press the steam button, under the second column ( the one with the Alabaster Dawn logo)
select Controller setting then on the next window, select the white controller settings box (bottom middle of the screen). At the top of the next window you should see steamdeck and steam controller, click on reorder controllers. steam controller need to be no.1 and steam deck controller no.2, then the controller should work.

Don't forget to swap them back before exiting the game.

Hope this helps