Let me reply to myself in this topic. I am apparently mistaken... Even in an older version - this is the case.
Interesting enough.
The problem seems to be in SSH - as I cannot SSH into a client using the root account anymore and had mistakenly thought the isse was related to the ROOT account GID not mapping properly.
I could swear in the past that this was not the case.
So I guess I have an SSH issue with the new version of Centrify Express - which of course has nothing to do with the above.