Thanks for the good questions. The decisions in both of these were driven by the fact that most people will be hand tapping these holes (at least I was). The counterbores are there to remove some material so you are not tapping the entire thickness of the stock. If you are not 100% straight when aligning the tap into the hole, by the time you are 3/4" deep into the material the tap is going to be hard against one side of the hole. A good recipe for breaking a tap, which is never a fun thing. By reducing the thread engagement, even with some misalignment you shouldn't have a problem. If you have equipment available to tap cleanly all the way through the full thickness of the stock, then sure, go ahead and skip the counterbores. They are an insurance measure for those of use with nothing but a tap and tap handle.
I should probably put "counterbore" in quotes, since it they don't need a square bottom shoulder. Maybe I should call them "relief holes" or some such thing. You can just run a larger size drill bit part way into the first hole to remove some material. The exact diameter isn't crucial either. As long as it is a bit bigger than the diameter of the threads. Actually, I suppose even if the counterbore were the same 1/4" diameter size as the tap, it would still remove enough material to give some relief against the tap jamming.
I spent some time carefully marking all holes on the aluminum parts first, so then I was able to drill all of these holes out in one operation. I just set the depth stop on the drill press and went through one part after the other. It just took a few minutes to mindlessly drill all of the "counterbores," and a few seconds of setup time.
I used studs since they put less stress on the threaded aluminum holes. When a stud is tightened, the primary force is one of pulling, whereas a bolt in that same hole is both pulling and turning against the thread faces. By transferring that force to a steel nut rotating against steel stud threads, you can get much higher clamping force without worrying about the aluminum threads galling or stripping out. If they weren't hand-tapped holes I'd be less worried about this, but in general I do like to put studs into aluminum. it just seems like a good practice to me. Bolts into aluminum make me very worried, unless the required clamping forces are low. Stripping a hole while tightening a bolt would possibly be even more annoying than breaking a tap in a hole, since at that point that part has already been completely finished.
Since I'm the King of Cheap I can relate to your frugality, so if you figure out any ways to shave any cost, please let us all know!