Well, that's one thing with Flatpak. There is a permission system, as the applications are fully or partially sandboxed. You can install "Flatseal", that can change permission for each installed Flatpak application. But it can be confusing or hard to understand what you have to change in order to make it work. Or maybe the application itself is not packaged correctly as a Flatpak, I don't know.

I don't like flatpack for the exact reason of this thread. The serious distros already do quite a good job in orchestrating their libs and other packages so that all works together.

Flatpack in theory is supposed, when well configured, to have little niche environments for some packages to work sandboxed and with their little special dependency chain.

In practice the knowledge and fiddling necessary to have this work correctly is akin to do it directly and safely in the main environment. People are encouraged to use flatpack but it is not a "just works" installer, unlike the default package manager of any serious distro.

That's why I don't use flatpaks, either they're not accelerated, or they can't use external libs already installed, or they can't print etc etc. Sure, that's all fixable if the devs were doing a good job on flatpaking, but they don't, as it's quite complex. So we end up with apps that have a reduced featured set. I personally prefer appimages, even if they're a pain to update manually (from official sources always). I have about 10-15 such apps that I update them once a month manually. Everything else is from the official repo.

More details on your GPU and how you installed your drivers would be helpful to understand your issue. You should not need to explicitly enable GPU permissions in every flatpak as some of these comments are suggesting. That is to give apps direct GPU access, which is not necessary for hardware acceleration. A lot of the info in this thread is not accurate.

My best guess is that it's not a Flatpak permissions issue as others are claiming; the software is just trying to use your iGPU (which is usually crappy) instead of your dGPU.

Try taking whatever command you use to start the program and tacking DRI_PRIME=1 on the front. This has often worked for me on applications regardless of whether they're native or Flatpak.