If you go into the advanced options in the controller settings, there’s an option that let’s you configure the desktop controller mappings. This only affects the actual desktop though, not desktop apps you launch from the plus menu.
Also, the ‘Enter Gamepad Mode’ thing doesn’t seem to do anything? I installed Super Tux Kart from Flathub, but entering gamepad mode just made the controllers not do anything.
I did some more testing and they only apply when you’re in ‘Gamepad mode’. Otherwise you’re stuck with the default pointier mappings, which only uses one controller while the desktop one can use both.
Also I found out that the controller config does apply to apps launched from the plus menu (when you’re in gamepad mode), but this doesn’t work for Flatpak apps (sandboxing issue presumably).
That reminds me of another random issue I had: I can’t point using one controller and use the stick for the other controller to scroll. On the Steam Deck, it feels very natural to point with the right touchpad and scroll with the left touchpad, so I figured it would feel natural on the Steam Frame to point by aiming the right controller while moving the left stick to scroll. But any time you move a stick, that controller becomes your pointing controller.
Yeah, I expected the scroll to work the same. The current desktop integration seems really half-baked.