Typically the front sight heights (OAH) includes the nominal 3/8 dovetail base (about .090") of the whole thing, even though the real 'blade' or ramp and 'blade' height is above the barrel top surface.
FWIW, I like to have the front sight height -0- out at about 100yds with the rear adjustment no more than about 1/4 of the way up. This gives me some fine tuning 'down' adj. and still gets me the longer range high. When Ive tried to get the front/rear set up to be on at 100yd. with the rear at its lowest setting I often have wished I had a little more down to go. I have made mock up front sights with a 'ramp' of wood taped on the barrel with a finishing nail as the post & bead. This lets me find the right height of available sights ( remember, above the barrel plus that .090") to get it just so.