If this is true, and I trust you on that, shouldn’t it then be a reason to advise users that they should not upgrade from a system package to a flatpak at all, and/or only install flatpaks when they’re fully aware of their limitations?
When I search for Gramps in my software manager, on LMDE 6, it shows a system package for version 5.1.5, and a flatpak for 5.2.2, and if I didn’t know beter, it would be quite logical to choose the latter. And that is, because there is no information about possible limitations of the flatpak version, and maybe the maintainers of the Debian repo don’t even know about these. And I bet that many programs run quite well in a sandbox, so there is probably no reason to give a general warning. And AFAIK, flatpaks are often easier to install, because they bring their own dependencies, isn’t that right?
For Gramps, we know that there are limitations, like in the sense of access to hidden folders like ~/.gramps, and maybe some others too. I read about those, in other threads, but since I never use flatpaks myself, I don’t know what they actually are, and this graphic thing is completely new to me.
And in this case, the system packages are available, and the .deb files labeled as fit for ubuntu can also be installed on Debian, and LMDE 6, and MX 23, because they’re all based on Debian 12 a.k.a. bookworm.
And of course, if users prefer flatpaks, it helps if we can provide information about where they store files, and what they can and can’t do in other areas, like GUI, and maybe networking too.