Also flatpacks don't show up either.

To me, that would be far more useful than how it currently functions.
It would be nice to have tabs for "all installed packages", "user installed packages" and maybe some other tabs such as "flatpacks" and "downloaded packages"; with the option to input a path for the downloaded packages for re-inetallation.
Then you could give the user the option to un-tick individual packages or entire tabs/sections.
IMO this would fulfill the presumed aim of "user installed packages" much better; i.e. making the process of upgrading from one major version to another as seamless as possible.
P.S. I also wonder if, in the long run, it wouldn't be better to roll this functionality into the MX package installer itself.
P.P.S - I hope this is classed as a "non-package feature request" - if this is not the right place to post this, please let me know. Many thanks.