Graphics drivers in Flatpak have been a bit of a pain point. The drivers have to be built against the runtime to work in the runtime. This usually isn’t much of an issue but it breaks down in two cases:
If the driver depends on a specific kernel version
If the runtime is end-of-life (EOL)
The first issue is what the proprietary Nvidia drivers exhibit. A specific user space driver requires a specific kernel driver. For drivers in Mesa, this isn’t an issue. In the medium term, we might get lucky here and the Mesa-provided Nova driver might become competitive with the proprietary driver. Not all hardware will be supported though, and some people might need CUDA or other proprietary features, so this problem likely won’t go away completely.