Solution: tried native steam and worked instantly. Fiddled around with flatpak permissions and discovered steam need all devices access (rather than just input) for the controls to work when streaming to the deck.

I wanted to stream Expedition 33 to my deck. The game launches just fine but it won't recognize anything but the touch screen and I see MnK controls are active.

So I connected a controller to my PC, launched the game there, then started streaming from the deck. But as soon as the deck is connected the game goes back to MnK inputs and again nothing but the touch screen works.

The PC is running Steam Flatpak and Proton Experimental. With default Steam Input settings (which I think cannot be disabled when using Steam Play anyway).

I cannot run the game using Proton GE, just getting a black screen with audio.

So is Steam Play supposed to be a plug and play experience and I'm unlucky?