Flatpak is still not able to fully replace native apps in certain situations, sure, but that wont be the case forever. If Ubuntu believes they can replace debs with Snaps I believe someone can do the same for flatpaks given enough time.

Flatpak lets people host their own repositories, which is where I think we'll see distros becoming distinct if they DO choose to diverge from Flathub's selection, such as choosing to block non-free software. Over time, though, people generally all just add flathub if it isn't already available.

And, again, if you need something more finegrained than flathub, there's no reason why distro maintainers can't move to a nix-based infrastructure-as-code and you'll be free to host a repo with all of your distro's software packaged as code.

The power maintainers want over users is simply too much effort to justify as more apps begin to complain about packaging issues downstream, and apps become more complex to build. Users will inevitably bypass them. Devs will inevitably become hostile to downstream repacking.