Scott, if I understand your post, you're saying that if you use the lens at a setting of f/8, say on an f/2.8 lens, that's the same as a lens with a base aperture of f/8, in the way the AF works. As I've been grappling with this, that's what I thought initially.
I can be very wrong, about both your post and the way this works, as I'm just learning these facts about how the D4 and the D800 work, but it's my understanding that it has to do only with the base (max) aperture. I'm counting on the others to correct me, if I'm wrong, or confirm my understanding, if I'm right.
With AF and AF-S lenses, it's my understanding that basically, the aperture is wide open to the maximum aperture when focusing, and stays that way until the shutter release is pressed all the way down. At that time, the aperture stops down to the chosen aperture, until the exposure is complete, then opens up to the max aperture again.
Therefore, my understanding is what the lens is set to when the image is made doesn't count with regard to how AF is working. It's base (max) aperture is what controls the way the AF system works.