Flatpaks aren’t the cause of the fact that different applications don’t function correctly with different versions of libraries
This problem has been solved by Nix and Guix. Nix is as popular among developers as flatpak is. Add bubblewrap to all applications, and you get nearly all the features as flatpaks. Flatpaks, meanwhile are huge and a bit slow to start - problems that Nix and Guix don’t suffer from.
I do use flatpaks extensively. But they are probably not the best solution to the problems you mention.>