Even if you use Flatpak, you need XOrg / XWayland on the host system.
Fedora Kinoite/KDE and the KDE Plasma desktop on its own are especially annoying, as I have no idea how to turn off those legacy support services from constantly running, like XWaylandVideoBridge (never used) or XWayland entirely.
I think Windows is just too bloated to also use Containers. With WSL they found a good way and apps should totally run in containers, but this is simply not yet done.
VMs would suck for efficiency as they rely on CPU virtualization and GPU passthrough. The former will never give native performance