1) You use diameter of port rather than area because you're not calculating the force being applied over the ports area, thats not how this calculation works, its approximating the max flow for your bore. So if you're ported to 75% of your bores diameter, you're essentially making 75% of your bores potential power output in fpe for your current configuration (pressure/barrel length/plenum volume)...
Dont' want to clutter up the thread so will quote each point individually
If I have a bore which is .25 cal. The cross sectional area of the bore is PI*r2. Simple enough. So (0.125^2)*3.141592 is 0.049 sq. in. That is the cross section of the bore and the area upon which the pressure acts. The diameter of that bore is 0.25. If I had a transfer port which was also 0.25 inches the ratio of the area of the port to the area of the bore would be 1 to 1. That part is true. Again I hope, simple enough. Now then, if I had a transfer port which was .20 the ratio of the diameter of the port to the diameter of the bore would indeed be 0.8; however, the ratio of the area of the port to the cross sectional area of the bore would be (0.049/((0.1^2)*PI)) ... Remember we calculated the sectional area of the bore above so we don't have to do it again. The new ratio of the area of the port to the area of the bore is 0.64 to 1. In other words that ratio decreases much, much faster than the the ratio of the diameters. For example if the diameter of the port were half the diameter of the sectional area of the bore the ratio of the diameters is 1:2. By your reasoning a port which is half the diameter of the sectional area of the bore would develop half the power (would move half the air necessary to develop that power) you could get out of the bore. A calculation of the ratio of the area of said port (0.125) and the bore (0.25) using the method above works out to (0.049)/((0.0625^2)*PI) which ratio is: 1:4 for all intents and purposes. I won't bother you with the self-evident fact this is because the formula for area of a circle squares the radius. This means that a port which is half the diameter of the bore will always have an area which is one quarter of the area of the bore.
Sorry for the long winded explanation of my thinking. Wanted to keep it as basic as I could and make sure I hit all the salient points. Some things are just not obvious to me and it helps me to work them out long hand. Check the math if you wish, there may be errors. The one thing I know by looking at the formula for calculating the area of a circle is that the area of a circle of radius 1 is four times as big as the area of a circle of radius one half. Basic geometry.
Now as to the exact effect of calculating energy transfer through a port into a vessel via a compressed fluid. I am not a chemist so I will simply speculate using the facts and concepts that I got in my chemistry classes, many years ago. We know that fluids under pressure will equalize across a barrier that has a port in it. We know that there is turbulance around the edges of the port as the fluid literally bumps into itself and the port. We know that turbulance extends into the surrounding fluid some distance and that eventually it gives way to laminar flow. This intuitively suggests that the relationship between the maximum volume of fluid a larger aperture will pass and the maximum volume a smaller aperture will pass is not linear. I assume you understand what I mean by "linear"? Not only that but that ratio becomes less linear as the size of the aperture is reduced. At some point practically no fluid will flow because of the turbulance at the port.
All that said, if you want to talk to someone who really, fully understands this stuff, you should cultivate an acquantence with Bob Sterne. If you are looking for a healthy discussion on fluid dynamics you need to talk to him, not me. I will say this though, I am fairly confident that I would be able to follow almost all of what he told me or showed me on the first pass.
Onward.