A few points I'd like to address:
Metapackages are being addressed in 16.10 by making pre-installed applications "Recommended". This'll make them safer to remove without taking out ubuntu-mate-core and ubuntu-mate-desktop with them.
I've removed pre-installed applications many times in 16.04 without any issues, I'm not sure why some users start having problems doing so.
You still can, there's got to be some defaults, otherwise I'd say a distro isn't that functional "out of the box".
Of course, that's the plan. 
It will also feature the pre-installed applications, so users can install/remove these default applications easily.
It's possible to put together one yourself, grab a mini.iso and install ubuntu-mate-core. 