I agree with that, flatkpak is very much work in progress. A lot of packages are still unofficial. Some software are also not meant to be sandboxed and do require access to the whole file system. I do think it is going in the right direction though.

The author is also mistaking Gnome Software (the gui for managing apps in gnome that has a flatpak backend) and flatpak itself. Marking the app as Sandboxed when it's not is a gnome software issue, not flatpak.