

And that is still largely true - I’m still running XFCE with xorg on Debian, and I think the only issue I’ve had was Waydroid.
Will there come a day where what you say is true? Yes.
However, right now, a more apt example to convey your point is systemd; that’s true for most distros with a lot of community support. Even then, its hold isn’t absolute - Alpine seems like the most livable non-systemd distro, though I could be wrong.
I’d take a well-maintained native package for my distro over a Flatpak, but sometimes, a Flatpak is just the the easiest way to get the latest version of an application working on Debian without too much tinkering - not always no tinkering, but better than nothing.
This is especially true of GIMP - Flatpak GIMP + Resynthesizer feels like the easiest way to experience GIMP these days. Same with OBS - although I have to weather the Flatpak directory structure, plugins otherwise feel easier to get working than the native package. The bundled runtimes are somewhat annoying, but I’m also not exactly hurting for storage at the moment - I could probaby do to put more of my 2 TB main SSD to use.
I usually just manage Flatpaks from the terminal, though I often have to refresh myself on application URLs. I somewhat wish one could set nicknames so they need not remember the full name.