I'm not certain but I don't think the AF sensor has anything to do with WB.
As far as I can tell the D4 & D800 have three sensors:
1. The main image sensor 2. The 91K-pixel RGB sensor 3. The AF sensor module (Multi-cam 3500FX)
Nikon's website seems to indicate that WB is done by a combination of sensors 1 and 2. It says: "With the 91K-pixel RGB sensor and the image sensor working together, the camera renders white as white with supreme accuracy." (Source page - http://imaging.nikon.com/lineup/dslr/d800/features01.htm)
Even if sensors 1 and/or 2 vary slightly between samples, surely any differences would be ironed out during WB processing. In other words all D4/D800 camera bodies must have the same set of fixed reference points built in, otherwise the K values in the menus (and p145 of the manual) are meaningless. In theory, 4K on my D800E should look identical to 4K on your D4 if both cameras take the same shot under the same lighting. Ditto for all other K values.