Thanks for sharing this; for people on atomic distributions this is important for getting things set up how you want.

I’d say though, if you’re not on an atomic distribution then I’d use native builds of Steam and Gamescope for your distro wherever possible. The overhead of flatpaks is pretty minimal in practice, but the faff of having to configure things is higher with interconnecting flatpaks. It can be difficult to problem solve errors and by default just generally requires more configuration work (like installing the Proton-GE flatpak) without much real benefit. A native install will largely involve just installing Steam and Gamescope and letting Steam configure it’s own versions of proton.

In addition there can be real faff in setting up controllers (as you have to pass udev rules through to the container) and the game data will be stored in the flatpak’s file system for the sandbox instead of ~/.steam (which can be annoying for modding but is manageable).

Flatpaks can fail without seemingly clear reason; in my experience they’re often actually working perfectly it’s just that the sandbox isn’t quite configured for what you’re trying to do. In my opinion for Steam, it’s an unnecessary added layer of complexity for little to no gain. Flatpak is great in many ways, but not ideal for this unless no other options.