The HDZ is narrower than the stock axis or Z-Plus — this affords greater movement along X (unless one is using a dust shoe option which makes the carriage wider). It is also thicker than at least the stock Z.
This necessarily alters the relationships of the carriage to the bed resulting in some shifts — remember, the machine origin is set relative to the top right edges of the carriage, and the back edge of the gantry — the actual endmill position is then an offset from that based on the geometry of the parts. I wrote a little bit about this at:
https://wiki.shapeoko.com/index.php/SO3_Function_Test#Distance_of_travel
and
Need to work up a nice file which shows all the relationships, so that I can make a nice fixture for cutting joints.