Yep, I just cut a fret slot in the bridge blank. Then shape the bridge and tap in the fret. There are two ways of placing the slot, one is to cut the slot straight so that you angle the bridge for compensation or angle the slot for compensation, so that the bridge stays straight, in line with the back of the box.
if you are talking about the fingerboard "nut" then the positioning or measuring would be off the centre of the fret, centre of a bolt and front edge of bone, timber, corrian nuts.
Hope this helps. Taff