The client has access to files and controllers, games don't

Testing my own build process for the mesa-aco as described here: https://discussion.fedoraproject.org/t/getting-the-new-mesa-aco-from-valve-using-toolbox-and-without-replacing-system-libs

Games wouldn't start because they did not have access to the files. I configured the override settings to provide access to the files directory and checked it was correct by navigating through it from the steam directory navigator for the screenshot saving place.

Seems like it could be related to this bug regarding gamepad support: https://github.com/flathub/com.valvesoftware.Steam/issues/255 where the client works nicely but then the games do not have any access.