You are thinking too much.
I always had it in my head that you are actually aligning the scope internal tube to the barrel axis, so as long as it is directly above, then it should run true to the barrel when altering windage. The vertical alignment you cannot get true as it is too far above to start with, and you actually want to try and follow the trajectory as close as possible at the ranges that you shoot at.
I am sure someone will now tell me I am wrong.
If that confuses you, now you now how I feel.