Yes I measure to center of bolt on the body mount and get dang near exact, but just like anything.. the farther back I measure the more it increases.you spotted the bumps equally and just made minor adjustments for the pinion angle, correct?
then it is what it is. once you lift the rig the connection point is lower in the travel arc this can position the axle slightly behind the upper spring mount until it compresses and then comes forward to spot right where you lined it to the bumps.
as far as that 1/16" try several points of reference not all are exactly symmetrical side to side always. and don't have to be equal since you spotted those bumps