I'm currently away and finding the experience on my steam deck really great out of the box! I set one of my back buttons to toggle the thing that shows interactables around you and looking forward to finding more little tweaks to do as I play.
When I tried this (default controls, mapping left alt to one of the back buttons) the game would pause while swapping to the mouse and keyboard overlay and stick to that until I hit another button. I wasn't able to move around while the overlay was swapped. Was this the same for you or did you map it in a different way?