I put my camera (D800) on a tripod to check for any focusing issues ,and if I switch from OVF to Liveview the focus dot is in a different location.I tried two different lenses and they both give the same results. My other dslr is spot on when switching between OVF and Liveview.
There are at usually two modes for Live-View on most modern DSLRs. One of these modes will use Phase-Detect AF which basically flips the mirror up to perform autofocus and uses the same points which is why it will coincide with the ones you see in the OVF.
All other modes use Contrast-Detect AF which is performed using the image-sensor which means it is completely unrelated to the points you see in the viewfinder. In fact, these modes can autofocus from a large number of areas and points, often many more than with Phase-Detect AF.
With the Nikon D800 and D800E specifically, Nikon has only implemented the latter while the old D700 had both, as do most other DSLRs.