Flatpak – a security nightmare
Cross-posting a comment from Reddit, because it nails one of the points mentioned:---The list on the page is    Gimp, VSCode, PyCharm, Octave, Inkscape, Steam, Audacity, VLC, ...

With the exception of Steam all of those programs are used to open random files anywhere on the system. One could implement a permission prompt for accessing a file, but that would lead to a Vista-like Situation where basically every action causes a prompt.Now, that's not to say this is good as it is, but for most listed programs it's probably the way to go.