You've got to remember, there's more to a lay out than just distance from PAP; you've got to consider the angle. You mentioned stacked, which would mean that the pin and MB are a straight line parallel to your VAL. That is not what the picture illustrates. If you sketch your midline on the ball, you should see a mirror image of the line from pin - PAP and the line from PAP - MB.
Hope this helped a little. That is why you will often see a layout represented by 5" x 4" with pin 2.5" above midline. Without the last part, that 5" x 4" could be pin over or pin under while still being 5". Take a compass (that draws circles) and set it to 5" and place the point on your PAP. Now draw a semicircle on the ball to the left (RH). Anywhere on that line is 5" from PAP.