>most desktop users find it difficult to understand, and often have bigger problems

That is exactly the strong point of flatpaks. It's a lot easier to use toggle in a GUI for permissions than write whole new profiles. Not to mention that many even disable selinux because it is difficult.

>An outdated old package library relies on people understanding/tracking the complete OS

It takes 0 understanding to copy paste a outdated package warning and report that to the repo listed in flathub. It explicitly tells you as much.