I don't like flatpack for the exact reason of this thread. The serious distros already do quite a good job in orchestrating their libs and other packages so that all works together.
Flatpack in theory is supposed, when well configured, to have little niche environments for some packages to work sandboxed and with their little special dependency chain.
In practice the knowledge and fiddling necessary to have this work correctly is akin to do it directly and safely in the main environment. People are encouraged to use flatpack but it is not a "just works" installer, unlike the default package manager of any serious distro.
