Doesn't appear anyone ever answered this question here, but in case you (or anyone else who comes across this) still want to know the answer, I think he mentioned what could be your problem in the video. The shrinkwrap modifier essentially "shifts" your geometry, so when you have that turned on, you're not getting a clean look at what your geometry is looking like. There was a few times where he specifically turned off the shrink wrap to make sure that he wasn't getting any distortions in the actual mesh. I think this is also why he primarily used the surface snapping (the magnet) for most of the initial layout so that he could avoid some of that and used the shrink wrap after he already had most of the needed geometry in place.
