It seems, after reading all of this, that the question of whether the two arrow groups should only be compared to each other or, also, whether the bare shaft groups should be compared to point of aim, has not been answered?
Why not just do as OL says and tune until groups hit the same point and then add or subtract shelf/riser material to get the point of impact to where you want it? I'm not saying that OL says to do this second step, I am. I realize that changing centershot will affect tune but it seems that one could work with it to get the perfect shot- a perfect arrow that hits where you aim.
So you tune to get groups hitting the same area, then shift centershot to move impact, then retune, and so on.......?