I’m far from an expert. But I think an advantage of Flatpak is in the case of different programs needing different versions of the same dependency. Flatpak keeps them sandboxed from eachother. And from your system. So if for example a program depends on Python 2, but your distro depends on python 3, you could install the Flatpak and not worry about it. Atleast I think that’s how it works…
Edit: I misread your comment. Lol I see what you’re saying now. My bad