Your system information

• Steam client version: 1788652215
• SteamOS version: 3.8.16
• Opted into Steam client beta?: No
• Opted into SteamOS beta?: No
• • I did not opt into betas because update logs for the last 3 months show no related fixes of this issue neither for Steam nor for SteamOS.
• Have you checked for updates in Settings > System?: Yes

Please describe your issue in as much detail as possible:

• This bug was reported 2 years ago for Steam Deck as [#10551 in steam-for-linux](https://github.com/ValveSoftware/steam-for-linux/issues/10551), but for some reason was closed with no response.

When booting Steam Machine in Desktop mode, starting Steam, turning the controller on and launching any game, the controller keeps its configuration defined by Settings > Controller > Advanced Settings > Desktop Layout instead of switching to game-specific configurations.
Take for example The Binding of Isaac: Rebirth (using Proton) and Factorio (using native Linux support). Launching any of these does not enable my custom configuration, and I still have the default Desktop Configuration layout.

Notably, everything works as intended in Gaming mode - layouts switch automatically between the game, the Nested Desktop and whatever other game you throw at it. So naturally, I expected it to behave the same in Desktop mode, because using Gaming mode for me is a bit cumbersome.

Steps for reproducing this issue:

1. Switch to Desktop mode (either from Gaming mode or by setting an automatic Desktop startup using steamos-session-select plasma-wayland-persistent in Konsole)
2. Log in to Steam
3. Enable the controller and connect it to Steam Machine through integrated connector or the puck
4. Launch a game with or without native Linux support
5. Check that you have a game-specific configuration (RMB on a game in your library > Properties > Controller > Controller Configurator) and that it's different from desktop configuration (it's usually gamepad-like)
6. Try clicking some buttons and trackpads and see how they get reflected in the game. The most obvious bad sign is if right trackpad still acts as a mouse, and triggers - as LMB and RMB.