Steve,
So you are saying if I probe z and set surface with that just a standard home z is all that is necessary, I am not sure why probing Z rather than just homing Z gives me a more accurate z height. It works well so that's all that really matters
I think you haven't grasped how MASSO Auto Tool Zero works.
When you home the machine MASSO moves to home position and sets it's variables to the home position setting you have supplied in the homing dialog, establishing the Machine Coordinate System (MCS) zero position. Then it moves to the ATZ position keeping track of where it is in the MCS DRO and then proceeds to "measure" the tool (T1) which is the last one that it "changed", when the ATZ touch probe is activated it records it's MCS Z position (TP1).
Now when you set Work Coordinate System (WCS) Z zero by touching off or probing, MASSO again records the MCS Z position (ZP0).
Next you change tool (T2) MASSO goes through it ATZ routine and it records the new position (TP2), then it calculates the difference between TP1 & TP2 and applies that to ZP0 so that the new tool's tip should be in the correct position when you goto WCS Z0.
To see how things change on the Z axis DROs, change to a long tool and zero Z axis to your work surface now move Z up to 10mm below Z home (MCS DRO -10) note WCS Z DRO reading. Now change to a short tool and again move to MCS -10, now compare WCS Z DRO to previous and it should be larger.
Hope this help you to understand ATZ.
Regards,
Arie.