Calum,
It would be rather unusual to use the spindle w/o a tool as the master.
Perfectly possible from a math and MSM standpoint, but generally not preferred. The reason is that this will make ALL tools longer than the master. Most people want the master to be the longest tool.
This is so that if you turn on TLO when you didn't mean to, the tools shorter than the master all move away from the work piece.
With the master as the shortest tool, they will all plunge into the workpiece - not as nice as the other way around.
This is covered in the MSM manual.
When you refer to Z0, you'll need to qualify - MC or WC?
Generally, MCZ0 is at the top, farthest away form the table and the TCP TP.
You measure the MT PTL offline (a positive number as it is a physical length that the dialog wants , not a TLO), and you have to use that value when finding the TCP TP MCz location. You did not mention that in your description - so I'm not sure exactly what you are trying.
The TCP TP MCz coordinate location will not be a positive number - it will be negative as it is below the MCZ0.
Please give the chapter on advanced tool handling another read before playing with MTM more.
I say that for two reasons - 1) it has lots of info that I can't repeat in a posting, and 2) if it is not communicating the concepts well, I would like to know why not, so I can improve the manual contents.
Dave