Well the pellets trajectory starts as it leaves the barrel and that's where the scope height should be measured at the end of the barrel, the crown.
Because in most rifles the barrel is either slightly pointing up or the mount rail pointing down which is required the scopes line is pointing towards the barrel and will actually cross it the further out you go and obviously that's extremely difficult to measure (A) because the scope can't really be measured at the barrels crown and (B) because you have a smaller tube inside the scope which may or may not be central and is what really needs to be measured.
What I do is...
1) Work out my pellet rifle combos coefficient by shooting through 2 chronos, 1 at the muzzle and 1 at 25 yards (I will shoot through both chronos at the muzzle 1st to make sure they are both calibrated).
Once I have BC I'll enter that into chairgun.
2) I'll measure barrel diameter and half it, I'll measure scopes objective diameter and half that too and finally measure the gap between top of barrel and bottom of objective.
Example, barrel 14mm = 7mm, objective 50mm = 25mm and gap 10mm.
7+25+10 =42mm 1.65 inch. I enter 1.65 inch in chairgun for scope height. I also enter the pellet weight and rifles muzzle velocity along with the zero, lets say 25 yards and scope click values which again are not as simple as 1/8 or 1/4, best to measure them!
Chairgun will now give you all the data you need, POI, clicks and so on.
3) I'll carefully zero my rifle at my chosen zero range (25 yards), then shoot it at 10 yards (also very carefully) and measure the point of impact from where I'm aiming.
For example if let's say my POI at 10 yards is -0.5 inch but chairgun says it should be -0.65 inch I'll tweak my scope height in chairgun, lowering it from the 1.65 inch I entered until I get it to read -0.5 inch at 10 yards in chairgun