In this case the issue is with 100% on flatpaks side that they decide to ship and download the entire nvidia driver again instead of using the one of the host. Note both snap and appimage do not do this, they use the nvidia driver of the host.

There is no reason to have to download the entire nvidia driver again, distros cannot modify it as it is against its license.

Also even outside of nvidia you are still going to have troubles in games with flatpak if what you are using requires a recent version of mesa