It's because Zoom / Jetbrains haven't stepped up to package their software as flatpak, so volunteers got in there. There's a flathub policy that a flatpak project will be handed over to the vendor to maintain if they make that request - which is definitely good, but the fact of those volunteers being able to do this (however well intentioned) is not.
Yep. On top of that, some people just straight-up don't intend to port their software to Flatpak. There are a lot of unofficially supported packages (or incomplete ports) that will remain that way forever, which really makes Flatpak no better than the AUR in many respects.
The biggest problem IMO is that Flatpak coupled itself too closely with Bubblewrap. Flatpak is missing many key features because of this (support for running services???), and it makes zero sense in the context of a modern desktop. Apps like Flatseal should focus on sandboxing regular applications with Bubblewrap rather than trying to manage all of the software on it's own. As-is, Flatpak is the last resort of packaging methods for all of my systems, even behind Snap.
