The 20MOA bases are indeed tapered so that your scope is set at a downward angle. This allows the shooter to reach out to farther distances. With a no taper base you run out of scope adjustmet for really long shots when you have extra on the bottom end of the adjustment that never gets used. It is wasted. An scope set angled down will optimize the turret adjustment where you need it and still be able to have down ward adjustment for 100 yards.
No you do not need to factor this in to your program nor your calculations. Just zero the rifle in as normal, use exbal as normal and forget that you have the 20MOA base.