This is a great question - I have the same question. Nikon states in their manual that, in Live View (LV) you can use Face-priority AF: "The camera automatically detects and focuses on portrait subjects; the selected subject is indicated by a double yellow border (if multiple faces, up to a maximum of 35, are detected, the camera will focus on the closest subject; to choose a different subject, use the multi selector)."
I've asked several people if Face-Priority works in Viewfinder View (VV) and some said yes and some said no. I asked Nikon and they sent me to their manual where it is still confusing.
To really understand it, I'd like to know how it works. Certainly in LV they are using the 16.2MP sensor to establish focus using phase contrast since the mirror is "up". The manual says that Face Priority only works in Live View but when I spoke to tech support, they said it works in Viewfinder View as well but you won't see the faces outlined by a yellow box. It does work well in Live View (LV) but it's confusing because LV uses the 16.2 MP sensor to focus and VV uses the autofocus sensor module (above the mirror) with TTL phase detection and the red square focus point is highlighted (if using AF-s single point focus).
My recommendation is to use the focus point in AF-S mode, single point (like the D3) to ensure you are focussing on what you want to be in focus. It's a shame that Nikon can't be more specific and outline for all of us D4 users how best to use this awesome camera!
I understand that the face recgonition works in Auto mode too which is frustrating as like you I prefer to shoot in AF-S not AF-A but I have tried it and it does seem to pick the faces out. I watched a demo where by holding in the small button on the front while turning the back main control up pops this yellow option line that shows an actual face icon in addition to a few other choices- in LV mode ( same button that changes the afs/ afc options)
Art is the only way to run away without leaving home.
It was on the Creative Live D800 workshop last week. The course did not have as much info. reagrding the D800 as I had hoped so not worth purchasing IMO but the FR option button was useful information. Here is the link.