If you have issues with your controllers with the flatpak I would try switching to the native package. There should be a .deb package for steam. If it doesn't change the behavior, then I would assume something else is causing a problem.
You can also install flatseal and try messing with the dbus setting, should be like half way down the menu for the steam flatpak. Since flatpaks are usually not given access to the entire system I could see it not having the correct permissions.
Glad you got it working! I turn that setting on for all my games and I honestly didn't even think about asking if you had it on.