I get the author's concern but there is nothing useful in this article. It's misleading suggesting that the problem is with flatpak when the problem is that certain applications aren't using its full capabilities, aren't configured correctly and are in need patching. Or in the worst case, might need a redesign to fit the sandboxing model. This needs to happen with any sandbox that uses this model, not just flatpak. There is nothing else that can be done about this short of suggesting users switch to a different sandboxing model like Qubes. (Maybe the blog author can try that too and see how it goes, or could develop their own sandboxing model just to see how hard it is on a complex system like Linux)
So, GNOME Software has included a "Permissions" field (which lists an application's specific sandbox holes) since - if I recall correctly - GNOME 3.34: https://i.imgur.com/lCGgA1B.png. Not perfect, but definitely better than pictured. It's a bit of a shame that people have to use older versions of GNOME in 2020, but then, it's nice that Flatpak makes it easy to run new applications regardless :)
Also, I was trying to verify the author's claim about a vulnerable libssh in the gitg package, partly because I was curious whether they'd bothered to report any of these issues upstream. Looks like that was fixed in May: https://github.com/flathub/org.gnome.gitg/pull/12. Similar story with ffmpeg: https://gitlab.com/freedesktop-sdk/freedesktop-sdk/-/commit/....
So, woefully behind schedule, but, how long was the author sitting on these? It would be more accurate, less irritating, and more persuasive if they simply talked about it after the fact: this happened, various things are wrong with it, it should be avoidable, etc.
