Sorry about being so late in answering, but I was out of email contact ("gasp") for the last few days.
1. Over-pressurization: Well you have a point, but I like to think of the penny as a constant pressure device- Like the regulator on compressed air tanks. The penny makes up for the vagaries of fabrication and the imprecision of construction, differences in fuel quality, etc. Kind of a built in fudge factor that make it a very forgiving stove to build and operate.
2. Priming: You are right about the inefficiencies of priming from the top, but I would offer that it is not a "waste of fuel." When you pour the fuel in the top you can set the pot on the stand and light the stove. The heat of the prime is immediately heating the stove AND the pot. So the penny stove is working like a tealight stove at that point. As the stove warms it morphs into a pressurized jet stove. I could argue that "priming from the bottom" is the waste of fuel, as less of that heat would be available to the pot. Side heat would be a little better. But top, bottom, side- it is probably not much of a difference.
More important to me is the "fiddle factor." - place the penny, fuel, light- is simple verses -unscrew the thumb screw, fuel, replace the thumbscrew, poor fuel in the primer pan or on the wick and then light-. Ok not a big difference, but hey I'm trying to make a point here :-)
Now, I have a MBD Mini Sith that I have used in the past and it is a great stove, but over time I found the thumbscrew thing a nuisance for me.