I'd say that's either 1) outside the scope of the package manager, or 2) mostly-solvable as long as your package manager allows you to specify "extra files created by the application that I do not install but I will want to uninstall."

That's also not what's being asked for here. The basic request is this: track which packages were manually vs automatically installed, and give the user the ability to remove automatically-installed orphans whose manually-installed reverse-dependencies are no longer installed. This is what APT does and it works fine 99% of the time.