Have you tried flatseal? It's designed for flatpak permissions

I will remark that that sounds like a distro issue - I use Arch and the drivers are just in the official distros, no need to add external ones. Just look up what you need on the wiki and install it.

That said, AMD will still probably be a better experience.

One thing you might notice is that flatpak defaults to "system" installs. Is your root system directory filling up? You probably want to start installing onto --user, as this will put things in /home where they belong and, by default, sandbox permissions away from root (that, too, can be easily changed).

Also, don't fear mixing different ways of installing. I use AppImage, Flatpak, the default app-get install method, and .deb. FlatPak at this point is the best, because it offers the ease of use of AppImage, but the flexibility and auto-maintenance of apt-get/Software Update. The only problems I've encountered were due to me not understanding that it was filling up my root partition by default...

I've been running Mint MATE for about 9 years. Love it to death.

Basically every app is sandboxed to some extent. That way you don’t get conflicting dependencies. Because I use this machine for work, game performance is a much lower priority than file system permissions and stability and for most typical workloads. MacOS does the same thing by default now and very few apps get access to the actual root directory.