Yes but it sounds like he is comparing the viewfinder square with what is displayed on the LCD screen on the back. They are two different things not linked together...at least not on the 5D3.
The red AF point markers on the rear LCD are not tied to the point in the viewfinder...though they attempt to show you which AF point was activated during the shot, they are not calibrated to the PD sensor.
Sounds like he's comparing the selected AF point with the red marker displayed during image playback (with that function enabled). While they're not 'calibrated' if the center AF point was used, that red marker will be dead center in the image. If the shot was taken with a feature under the center AF point, and that feature isn't under the red box on review, there's a misalignment.
Note that it should be tested properly - on a tripod, etc., since if the camera is moved between half and full shutter button press (unintentional focus/recompose) the camera doesn't know that (unless it's a Hasselblad) and that will appear as misalignment.
I doubt that these two modes have separate AF systems with different AF point locations.
Your doubt is misplaced. Phase detect AF (viewfinder) uses a dedicated AF sensor, whereas contrast detect AF (live view) uses the image sensor itself to determine focus (which takes much longer).