Most bowyers mark the center of the bow, put the grip just below it and the shelf just above it. It'd be best if you could put both the grip and the arrow both on the vertical centerline, but one can't be where the other is. So, they just try to get both as close together as they can and work the tiller so the bottom limb is stronger in order to compensate for everything being off-center. That makes the string measure closer to the riser on the bottom than on the top.

In other words, the string isn't parallel with the riser anyway. Some bowyers actually do put the shelf on the centerline, more often with longbows than recurves, but then the bottom limb is tillered even stronger, so that it measures even closer to the string than on a bow built the 'standard' way. .

Your measurements are exactly what I'd expect to see. Set your nocking point in relation to your rest or shelf - whichever you shoot with - adjust it for best arrow flight and accuracy, and then quit worrying about it.