"Mated" may have been the wrong word, as I asked Nikon to check the lens on the camera once they had adjusted the D800, and to clean the lens - I believe they do their testing on a 50mm lens (which by the way was the focal length I chose with my 24-70mm for my FoCal tests).
No, I haven't run FoCal on the 50mm yet, as to my eye, the results were fine (once I had dialled in +7 after my "dog" testing) - so I am not concerned that Nikon may have "set-up" the camera for one lens. My understanding is that if the camera is aligned correctly, with its AF system working within spec, than any anomalies would primarily relate to the lens, hence the ability to fine tune.
But therein also lies the catch - fine-tuning zoom lenses can be counterproductive, as different focal lengths may yield different AF tune numbers. Some advise tuning the lens for the focal length you normally use - but that kinda defeats the point of a zoom lens in my view - if I tended always to use a given FL then I would be using a Prime!! So, it's a bit of a Catch 22. My rule of thumb is to try and nail the exposure to get my required DOF - if I don't get it consistently then I would re-examine my AF-Fine tune settings for those conditions, and/or check the lens.
I will eventually put all my lenses through FoCal (or FocusTune), but right now I'd like to focus on photographing life again!
When words become unclear, I shall focus with photographs. When images become inadequate, I shall be content with silence. - Ansel Adams