Seems like the main thing that would need to be adjusted is the Z-Zero plate thickness--that's an option in the "preferences" menu of the fireup app. We set it at the factory--but you can tweak it (for example if you want to zero your bit off of the top of your tailstock--just run an alligator clip from the z zero plate to the tailstock body and change the height to whatever distance is from the top of the tailstock to the center.)
Only catch is the Measure cutter routine sends the bit to the location above the plate. If you open Macro #2 in fabmo, the very first M2 command sends the tool to the zero location. You could either edit that to match your tailstock location--or comment out the first two commands and use the keyboard to find your zero location. Probably better to comment out the C3 (homing routine) because the router will be in lower position for rotary work that will probably cause it to bump the tool base on the forward move.