Just to clear up a couple of points you've raised.. Chairgun doesn't assume a constant BC, it uses a "DragFunction" table and has 11 bandings for the drag when the pellet is travelling below 810 fps.
So essentially what it does is alter the effect of the BC 11 times over the course of the trajectory for a sub 12fpe projectile.
These drag tables aren't purely theoretical either - they're based on thousands and thousands of controlled real world ballistics experiments over the past couple hundred years.
Shimming of the scope?.. Chairgun asks for a parameter which is the Line of sight height above the bore. If you measure this correctly, that measurement takes into account Shimming, Barrel Droop and Muzzle flip as well as some other factors too.
I have more than a sneaking suspicion that P-Calc will use the same publicly available ballistics calculations as Chairgun at it's core. It sounds like P-Calc has some alternative methods of measuring the input values required for this calculation which is interesting.
It is true to say that the Line of sight above bore will change when you change your elevation turret and this is something that Chairgun doesn't take into account, which is sounds like P-Calc does.
However.. the difference to the trajectory that this makes is so slight that you'd be extremely unlikely to notice it in the real world.
Hey - if it works for you great. Really it all depends on what you hope to get from the app.
(btw - the wind game uses the same publicly available ballistics code as Chairgun and very probably P-Calc too, although it assumes you're shooting at the Standard Atmosphere, because I couldn't be bothered to add input fields for environmental conditions