Disclaimer: Someone in the comments pointed out that this affects Nvidia only. I don’t have AMD, so I can’t verify if that’s correct, but likely this is only for fellow sufferers of the Green Nightmare.
I had this issue for months. Randomly, the performance for games would be abysmal (I’m talking 5 FPS in 10yo indie 3D titles). Then it would randomly work again for a few days or weeks until it would become terrible again.
Turns out, the reason for that was that flatpak appears to cause trouble when the system GPU driver is updated, but flatpak update isn’t run. So when I did dnf update (and it updated the Nvidia driver) without running flatpak update afterwards, the performance would suck, until something (or I) ran flatpak update again.
So if the performance in games launched through a flatpak version of a launcher like heroic sucks, run flatpak update.
And if that doesn’t work, run
flatpak install flathub org.freedesktop.Platform.GL.nvidia-575-64-05 org.freedesktop.Platform.GL32.nvidia-575-64-05
(Replace the version with your Nvidia driver version, and in case of AMD, google whatever the appropriate way is to install the drivers for flatpak.)
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