More so, if the packages are so important as the original post mandates, then it would be against any common sense to include in them software that is obviously optional.
What do I mean?
For example, shotwell and hexchat both belong to the ubuntu-make-desktop metapackage. I uninstalled both, but for argument sake let us assume I want to keep hexchat but remove shotwell. According to the original poster that is a bad idea because I will compromise future automatic upgrades.
So, what is wrong with this picture?
Well, why are shotwell and hexchat in the same meta package then? Seems like an arbitrary decision of the distro makers that compromise my ability to take control of my system. If shotwell and hexchat are to be made default applications (and that is just fine. I have nothing against the idea of pre-installed applications), don’t install them together, as part of a metapackage. In fact, don’t use a metapackage at all. Just pre-install them individually. Give me control to decide what to remove and what to keep on an individual basis, without compromising my system.
Meta pacakges like ubuntu-mate-desktop and ubuntu-mate-core are really just a convenience to a tiny portion of the user base. I have not know anyone (not a single person) for whom arbitrary collections of software as metapackages have been beneficial, on any distro. Not one. Metapackages are great for other things, like keeping track of the latest version of a multipackage installation (think the postgres metapackage for example). But as a tool to force me into an application garden in my computer that is decided by the distro maintainers… no, please!