I've noticed that by default if I connect my controller (Dualshock 4 in this case but it also seems to happen with all the other brands, including the SteamDeck) Wine does recognize it to an extent.
If I open "wine control" then "Game Controllers" then I can see that my controller is recognized in the DInput section, but the most important one, XInput doesen't recognize it, and if I try to play a game in that condition, the game wouldn't recognize that my controller exists, it would work, but it wouldn't let me use the default controller bindings, and I would have to rebind every single controller button.
If you add those two reg keys:
wine reg add "HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\winebus" /v "DisableHidraw" /t REG_DWORD /d 1
wine reg add "HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\winebus" /v "Enable SDL" /t REG_DWORD /d 1
Then the controller gets recognized as "XInput" and then all games recognize it and let me use the default controller keybinds.
So my suggestion to the Wine team is to implement those two registry entries by default, so that people don't have to add them manually to add controller support to Wine, and that would mean that all controllers would work out of the box with the default Wine settings and registry, something that now doesen't happen.