Make an aluminum or plastic disc slightly larger than the largest bit you want to use.
Precisely measure the thickness of that disc (I’d use 1/8" / 3mm -ish thick material if I were doing it.)
Put that on the bitsetter button and zero bit.
Add that disc thickness to the Z-height.
Carry on.
Example:
Disc 1.50" diameter, [0.118in / 3.00mm] thick.
Put in bit and put disc on bitsetter button.
Zero using bitsetter.
Go to CM and manually add the thickness of the disc to the Z position.