Hi Toby,
It is fixed in the camera position which indicates the point that
is in the camera center and focal plane. If you used I&S it
should have been calibrated with the nozzle and Auto-Focus.
The difference between top camera and bottom camera, is that the
top camera is moved to the subject. Whereas it is inversed for the
bottom camera, i.e., the subject (part underside) is moved to the
bottom camera and focal plane, hence the Z is always fixed at the
position Z.
You can adjust it on the Position tab, but of course, that is not recommended:

Better reopen and redo the I&S solution:

> Have I caused an inconsistency by editing this in machine.xml?
Very likely. The UPP must match.
But redoing the I&S solution should fix it all together.
_Mark