It is really quite simple.
Flatpaks (and Snaps, and Appimages and Docker containers for that matter) are essentially designed for app developers who grew tired of distro maintainers demands to fix certain things about their build systems and their applications that broke when their apps were used on distros other than the exact distro and version the developer was using. They are designed to take a "kill the messenger" approach to the problem and now people are wondering why the work that the distro maintainers did before doesn't get done any more.