sudo apt autoremove very regularly. This command removes all packages that are marked as "automatically installed" and that are no dependency of any other package on the system. It also automatically removes older kernels, except the last but one, so that you always can revert to the previous kernel if needed.
For your freshly installed Mate, it will be perfectly safe to run the autoremove command.
There is a potential risk when you removed metapackages. A metapackage is a small package that contains no software on its own, but that contains a lot of dependencies that are pulled in upon installing the meta-package. Typical examples are the desktop packages such as
xubuntu-desktop, etc. There, indeed, you are relying on whether dependencies have been properly marked as "manually installed".
In practice, in my test, removing
ubuntu-desktop followed by
sudo apt autoremove would not remove any packages. That means that the "top level" packages that depend on
ubuntu-desktop were "automatically" marked as "manually installed". It is different if you install a second desktop: in my test,
autoremove after removing
xubuntu-desktop, which I also have installed, would remove the whole xfce desktop, meaning indeed that in this case, all packages that were pulled in by the
xubuntu-desktop metapackage, are marked (rightfully in this case) as "automatically installed".
Bottom line is that some caution is always warranted. Always check what will be removed. However, in no circumstances will you break your system. You can always reinstall what was removed. In case of the desktop metapackages, you can always reinstall. They remain your safety net to restore all essential components of a desktop environment.