I've come to realize the topography of the flyover perhaps isn't clear because the movie doesn't explain that their "conic section flight path" involves flying around V'ger in a non-treatening manner and approaching it from the rear (instead of interecpting it head on like the Klingons), so the first view of V'ger is the rear of the ship, and the "maw" is actually the front. This is explained in the novel, and obviously properly communicated to the FX team, since the flyover is from back to front.
This is somewhat pertinent issue in the film that is indeed under explained. My solution to this is to excise the tactical shot that appears after Kirk orders the course change, and replace it with one similar to the Regula tactical from WOK whereby the virtual camera switches its viewing from the side of the plot to the top. This way I can have the course line articulate to the audience how the ship will come parallel to V'Ger.