Remote play together and steams controller management are two separate things.
RPT creates a tunnel to make everyone appear in the same session.
For controllers, especially in Linux check that you have the correct settings enabled eg. Enable PlayStation/nintendo support vs the default Xbox emulation.
I’ve personally never had any issues with RPT and controller settings after checking the controller is setup properly in Steam.
Dyson Sphere doesn’t support cloud saves, not an issue with the Steam Deck.
I’ve also had some issues with Fez but find it works better now