Well, these results (both FoCal and your own test shots of your dog) clearly show that in this case Nikon has managed to fix the issue.
I don't think many people would expect ideal operation since we live in a real world, but having less than average performance is definitely disturbing.
However you mentioned that Nikon has adjusted your 24-70 to work with the camera. While this is good, I wonder if other lenses perform relatively well with the camera now. Did you try any other lens to see how focusing works after the adjustments? In my case even 70-200 @2.8 shows the softness of one sensor group (in my case center sensor is very soft after the adjustments).
I would find it alarming if each and all lenses need to be "mated" to a particular camera using Nikon's service as oppose user-driven AF fine tune operations.