Everything else being the same, when I add more MOA compensation to the mount, I reduce the clicks by an equal MOA amount, in order to keep the poi the same. It really is as simple as that. Nothing would change in whatever ballistic app I’m using.
However, adding compensation to a scope mount usually results in at least a slightly different scope height. You must remeasure and enter the new correct scope height value in your ballistics app. Measure it near the scope gimbal. If you take the scope height measurement at any other location, you are on your own, because the math will not work in that case.
I know why I wasn't getting the correct numbers.
On the flat scope mount I was zeroed at 25y and was at 65 clicks for 55 and 60 for 10 yards. After moving to the 20moa mount I zeroed at 25 yards but shot to verify from 21 to 29 yards, there was very little difference between the zero at these distances. If my rifle shoots a 1/2" at 55 yards its going to shoot a 1/4" at 27.5 yards. I could not tell if 25 or 26, 24 or 27 was the true zero. I set it at 25 and moved on.
I measured the scope height, it was essentially the same (to within the calipers ability), so the old numbers in CG were correct but they did not match the clicks I had gathered with the new mount. On the new mount I was at 60 clicks for 55 yards and 59 for 10 yards, bringing me out of a full rotation for 55 yards (12 ft-lbs).
If I could calculate a pure zero point I would assume the two would be different, but in CG moving the zero point didn't account for the differences in the new mount at 55 yards. I had to fudge velocity and scope height to tune up the app to match my collected data.
And there is an overall point to this for this thread, in theory the triangles are the same, but with groups sizes around 1/4" at 25 yards using an inaccurate device to find a precise zero just isn't possible. Often in FT you need to create a work around to get things up and running, I typically question/doubt anything I have done like this until it proves itself in the filed. But to get out there and try it in the real world I had to let go of the fact that i'm not matching the CG results/theory for whatever reason (in this case a bad collected zero point).
Imagine what would happen if you had a bad chrony... Nothing would make sense in CG. And thus the reason why I had to use two profiles to get my clicks to work. 5fps, not a big deal, 30fps is problematic. Luckily mine was reading low or I would have risked being DQ'd at a match. Don't cheap out on your first chrony like I did (however it wasn't cheap), or if possible test it against a bunch of different units to see where it reads.