I dont own a scope that has the reticle in the center. It is usually well back toward the eye piece. But the center would appear to be a logical place to start. You would just have to remember to add the moa increase from the start if you use a ballistic table or program.
Actually, you don't add the MOA on the base to a ballistics program, at least not the ones I use. The tapered base just allows you to use more of your scopes adjustment to dial up. By mounting on a tapered base, the crosshairs are positioned more to one end of their travel, allowing you to dial up more elevation to shoot the longer ranges...
Center of tube at knobs. That is your reticle center. That won't really change that much with a 20 MOA base vs a flat base, but the angle you're looking down the scope does...that's how you get the extra 20MOA of adjustment on the base...
The input of sight height above the bore just gets you in the ballpark, anyway - you still need to go shoot your drops
In my opinion all external ballistics measurements should be made from the rifles muzzle. That's the point where the bullet starts to drop, and that's the point where the computations for atmospheric drag begin to be applied in external ballistics programs. For the purposes of determining the bullet trajectory relative to the line of sight all ballistics programs I know of are doing their calculations relative to the muzzle, and (in my opinion) the proper scope height to use is the line of sight from the optical center of the objective lens to the target center which is at the rifles zero distance. That distance can be anything the shooter chooses. The "scope height" is the vertical distance between that line of sight and the point where the centerline of the rifles bore intersects the plane of the crown.
A wedged base really has nothing to do with it as that may be canceled by an offset reticle in the scope. The line of sight does not have to be parallel to the optical or mechanical centerline of the the scope, but the optical centerline and the line of sight to the zero target will intersect within the objective lens. The scopes tube will normally be centered on the optical centerline but that's up to the scope's mechanical designer, not any law of optics.
You have to measure somewhere to have the input into the program, so I was just stating where I standardized on. I didn't say that I was measuring on the reticle, but rather trying to measure on the centerline of the line of sight.
Do whatever you want - it all still has to be shot out anyway.