I think most of the default software gets installed as one large package group, rather than as individual pieces of software. Only the group is marked as manually installed, but the individual programs pulled in by that group are marked as automatically installed. If you try to apt install something you already have as part of the default distro software, you'll usually see a message saying something like "marked as manually installed."
When you go to uninstall one program from the group, that one program is uninstalled as requested, but the group itself has to be marked as uninstalled, since you've removed one of that group's "dependencies" and thus can no longer satisfy that group's installation requirements. You now have a load of software that was automatically installed as dependencies of another package, but are no longer dependencies of any manually-installed packages. The next time you run apt autoremove, it'll remove all of those automatically-installed components and leave you with an almost bare system.
