BCs are AVERAGES
Averages determined at 300 yards, which is the shortest possible range you can actually use. BCs are not wrong, just not static, they are dynamic. They are based on Muzzle Velocity, they are affected by a host of things including the powder used, the rifling and then there is Shooter input into the shot.
A computer cannot fix your bad fundamentals, a computer cannot predict when you broke the shot at a weird point in your breathing. A computer cannot fix the cant you induced in your rifle while firing. The Human Factor is Real.
A BC is a starting point where the end user can if one so chooses to true and fine tune the number for their rifle system.
As been noted,
Scope Calibration is the biggest point of error next to shooter induced errors, if you have not tested your scope, you cannot complain about software being off.
Your 100-yard zero has an effect, are you Point of Aim, Point of Impact or is there a small variation in it. See Hornady True Range Zero for more details
The cant in your scope rail is .11" from front to back if you think .11" is the culprit it is probably you.
You cannot align the rifle to the computer, the computer must be trued to what your system is shooting. In other words, you have to collect the shooting data first and put it into the computer after to true it. You cannot simply take the computer and hope your rifle matches it, because it won't. Truing is real and how you go about it matters.
You adjust your Muzzle Velocity 600 yards and in, and you adjust the BC 600 yards and out to fine-tune the program. Depends on your range and how far you are shooting, but you have to know what you are doing.
The bullet maker is not lying, is not making up numbers, it's just those numbers are an average based on a certain set of conditions and a specific rifle system it from fired from. BCs are FLUID they should be adjusted for your system if you want them to be accurate.