I would agree with all of your observations including the reproducibility of live view. I have read (and experienced) that you will get slight variances when focusing fully racked from infinity versus minimum range using auto-focus - purportedly due to inertia of the lens elements or something to that effect.
I have also found that a shorter prime will tend to show slight discrepancies more than longer lenses or zooms...especially less expensive primes shot wide open (e.g. 50 f/1.8 D).
I have done the test with a setup to show back/front focus and found that different focus points will show variances from the center point but all (presumably) within tolerances. When I went back and tested my D700 I found a similar behavior. I think the resolution of the camera exposes a lot of the underlying systems (i.e. focus, lens, etc.).
Once I was able to assure myself that I didn't have an issue, I was able to fully enjoy the camera and just go take photos.