Yeah, Flatpak installing user-space driver for itself is unfortunately not solvable until there’s open source driver that is part of the Mesa project. Every time you update the driver in your system, Flatpak must update its nvidia-utils too, because their versions must match exactly. For Mesa drivers, Flatpak also installs the drivers as Flatpak, but they’re compatible back and forth and it only updates when it ships new version.

The cleanup should be more automatic, but try

flatpak uninstall --unused