From my experience, I have always measured from the top of triple tree to cap on top of fork. Can't see where it matters as long as you use the same measurements when removing and installing them.
Hope somebody that actually knows chimes in...
I've not done the bagger forks on the later bikes that utilize upper pinch bolts but imagine it is close to the Dynas.. I simply set the gap between the fork cap and fork tube even with the top of the upper tree and tighten the pinch bolt.. You can probably set them a little higher if you want to lower the front but there might be clearance problems between the crash bar and front fender if you raise them too much.. Use a scale (ruler) too set them the same on that case...