Nikon manuals are often not written with a great degree of technical precision (whoever wrote or translated it was not an engineer who fully understood the problem or did not notice the result is ambiguous).
The subsection concerns long exposures and high ISO settings, they do not say that these VR lenses should not be used at short exposures or low to medium ISO. This could arise when there is extremely little light from the subject and an artifact which previous cameras were not sensitive enough to see could now be seen as "fog". I would guess that the last sentence "We recommend turning VR off when using other lenses." to be an error. If they had written either "We recommend turning VR off when using the lenses listed below for long exposures and/or high sensitivities." or "We recommend turning VR off when using any VR lens for long exposures and/or high ISO settings." depending on whether all VR lenses cause this effect to some degree, then it would be more clear what they meant.
It should be easy enough to test the effect though it doesn't make sense to use VR for long exposures in any case. If the listed VR lenses cause fogging even when VR is off, then it seems like it could be annoying problem.
I would think it is straightforward enough to test. Set ISO to (say) 1 million, go to a dark room with all lights off. Test pics with listed and unlisted VR lenses with VR on and off, and see if there is visible fogging in some but not all of the images.