To visualisewhat is going on, draw an arc across a piece of paper, then lay a straight edge parralel to the arc across it.
The arc represents the bullets path, the straight edge is the scope line of site. As you change the hieght of the straight edge the contact points along the arc change. Tilting the straight edge will also move the contact points.
By changing scope hieght and angle on the bore you are altering how the line of site and bullet arch intesect. Where the line of site and bullet arch intersect equals 0 hold over, past that point adds hold over and before that point adds hold under.
Not sure if that clears it up or foggs it more but that is what your ballistics program is showing you.