Not that hard to stop wayland or xorg at the launch of a given application and restart it at that application’s exit. Of course, I only did it on the Raspberry Pi because the hardware lagged horribly running such apps with a gui/compositer/desktop the app wasn’t using in the background, but it wasn’t hard for me to get working, and its exactly how we did things with DOS apps and even some Windows games back in the WFWG 3.11 days.
Basically, there’s no technical reason the host operating system should have to be providing say X, KDE, Plasma, Gnome, Gk, Wayland, whatever, to a flatpack app that needs those things. Yes, the result is a larger flatpack, but that’s why flatpack’s do dependency consolidation.
Unless … Unless, you just really want to to run your games windowed with smooth window-resizing, minimization, maximization, etc.