Correct me if I am wrong and not on the same subject, you think that if some type of measured relationship from the scope lense to the muzzle end is given it would make the ballistics apps more precise in relation to scope height? You have brought up something that I've been thinking about for a while now... Scope height matters and is hard to pin down with a precise mechanical measurement when angled rails, moa mounts, erector tubes, and lense location and dialing are involved, but it may be figured out backwards...
Albeit maybe in a bit different context because I have not been thinking about the relationship to the end of the bore for this, but instead somehow using the actual starting point of the arc to then get a true scope height measurement to plug into the app. This "beginning" point of the arc, somewhere just behind the shooter, seems like it is the basis for the app's ability to figure out the math and the scope height somehow gives it a reference to this point in time. A complete arc along a line. Line of sight being a constant, the arc starts somewhere by or behind the shooter and ends at the given target yardage at point of impact, the scope height sets up this arc's relationship to the trigonometry math in the app so a precise dope solution can be given to adjust the angle of attack of the arc to meet POI.
So what I was thinking, but haven't done the math on because that's not my suit, is true scope height in relation to the bore can likely be found by doing "backwards math" from the point of impact back to the scope using other known yardages, and thus finding the start of the arc. And so somewhere just forward of the start of the arc is the true scope height.
Backwards math from point of impact, and impacts at other closer known distances, coupled with projectile speed and bc, should give the location and height of the scope to bore centerline at the lense, and could also give you the location of the bore end and it's relationship to the scope line of sight. If I am thinking about this correctly, it's going to be in the math.