Scope height has a huge effect on the numbers and if you have a riser rail with a slope then Chairgun doesn't work it out. Make small changes to the "height" value you enter and compare the numbers with what you found on the range. That usually gives you a basis for experimenting with other values e.g. 10 fps difference has a very small effect.
Scope mag is only relevant to the image you get when you select reticle i.e. holdover but quit useful when pondering on how much did to give it.
End of the day, the software predicts trajectory based on input data, hole in a target at known distances is real data (you may wobble, etc) but 5 or 10 pellets hitting the same horizontal line is the best measure of vertical hold or clicks.
The advantage of range testing is that you can deliberately add or take off a couple of clicks and see just what difference it makes.