" ...does not factor in inertia of either exhaust or intake flows and their results...it would seem the dynamics should be added into the consideration. "

Where is the inertia coming from? There is none in the intake, because it has a partial vacuum in it, so no real airflow travelling inwards relative to the size of the port. There is very little in the exhaust, because not much air/fuel is going in to the cylinder and then the majority of the exhaust comes out when the exhaust valves opens.

Let's look at overlap, with a C cam there is about 60° degrees of overlap. If you look at the piston, it virtually moves nowhere for the middle 20° while both valves are off the seat and you are at part throttle, so you have the vacuum from the intake port sucking exhaust backwards from the exhaust manifold, leaning out the mixture with O2 from the exhaust + additional O2 from the cracks.