If your Crown has a 20 MOA rail that could be affecting the "scope height" from Chairgun's point of view, I think. But what I do is put the best scope height I can measure into Chairgun, shoot groups at a bunch of ranges and then compare Chairgun's results to my shooting. There are many errors that contribute to differences. I think they include the BC, the muzzle velocity, the scope height, my shooting (with respect to the zero and the groups at various ranges), and the actual range to the target (I use a steel or fiberglass tape depending on the range). So I expect to juggle the BC and the scope height as well as the zero range to make the chairgun results align with my shooting results. I do not expect precise alignment, but I don't want it to match at 10, 11, and 12 yards and then be off at 50 yards. I want it to match pretty well over the entire range from 10 to 50 yards. Once I get this aligned, I save that Chairgun for future reference and print up some range cards. I think using the Chairgun results, aligned to my shooting results, is more accurate than just using my shooting results (in large part due to uncertainty about my shooting results). The one thing I don't really worry about is the math in Chairgun. I guess it could be wrong but I really doubt it is.
I appreciate that the OP tried hard to put some good inputs into Chairgun but I also submit it's pretty hard to be super precise about scope height, zero range, and shooting results. But I agree the differences are surprising. I'd try messing with the three inputs I play with to see if you can at least get closer.