You have a point here indeed. But it is much easier to create a CLI tool that combines the updates of all systems rather than destroying the incredible things that flatpak and pip offer. A five-line bach script would do. Although, a reliable distro would probably want to rely on something much more elegant and harder to break. For Fedora specifically, the python-based dnf tool should be straightforward to be extended to do that. Perhaps the Debian apt tool has a lot of functionality to carry on and may be harder to do. In the essence of unix philosophy and modular approach, it should be a separate tool. I’m looking forward to that too.