If you move the Wincnc probe you will be re setting macro parameters, do not do this..The probe is most likely set for the other 99.8 % of the bits you will use for center of bit
I am gonna presume you have an ATC because with wincnc you will always set table top z zero using the table.
I still use a 1.25-1.5 mortise bit takes a few more minutes to machine the flycut But hey...
To top set a bit with wincnc
When ready to set z zero lower the bit to an 1/8th above table top, then the tap lightly the "page down key" (if you are using keyboard) and or pendant if you have one,
slide a piece of copy paper under the bit. slide the paper back and forth til you feel resistance, then one more fast small tap. type in G92z0 or use the screen icon for "set z zero" if you have one.
With what ever machine you purchased you saved a good 6-10 k in cost. that said the heavier industrial controllers have their place, features and cost. for me I started using wincnc machines in 08 and have owned 6 since and have 2 now.
Wincnc is a excellent and stable controller there are a few nuances and this is one for the cost I am willing to live with it.
on the other hand it is fully capable of all kinds of stuff, my best guess is a Macro can be edited to do this offset. most manufacturers who use it will refer you to WINcnc directly for this as it is a control item. I do know some who can do this.