Speedmaster head hypothetical

Not saying your right or wrong, I've never ported a set of heads in my life, (why I'm glad your sharing your progress) but seems to me with lot of porters the throat size is the starting point they seemed to have sizes for a given application same with short side csa and pinch csa and the taper angle out from the short side csa.
You are correct that most porters assign a certain % to a throat size. That is because it is quite difficult and time consuming to find what works then to manufacture it, especially if bottom cuts are not concentric with the valve seat and top cut. The purpose of the bottom cuts and blending is to transition the air from the port and set it up for the chamber beyond. The chamber is all different shapes and angles. To make the best throat, it has to be customized as well.