People get headaches from 3D because of the difference between *actual* and *perceived* focal distances. It seems reasonable that the effect is different depending on whether the actual image is at screen distance or goggles distance.

But it's for this reason that 3-D didn't take over "all movies" ... and it's also one of the reasons why VR goggles, even if there's a nice little market for them, aren't going to become as ubiquitous as smartphones.