For just changing head transform I would not suggest to separate it into a new skeleton.. you could just get the head bone and manipulate its transform however you need. IF you think that the values may interfere with animation values itself. just create a new bone under the head, set values to 0. and control that from code. Note that no keys should be set for that bone.(so you will have a combination of 2, animate head how you wish in same skeleton, and control it from code)
However there was a game that we were forced to separate head as you did, since we were adding totally new heads randomly.
In unity there is a BoneFollower script within the Spine package, check it
But you can't make skeleton to follow a bone of a different skeleton in Spine editor.. there are no ways to achieve that even with constraints. I maybe I dont know.