Even in flat/Super 35 films, VFX shots would be cropped (at least in the post-Star Wars era). Since they were generally shot in VistaVision, which had a negative ratio of 1.50:1, they would be reduced to 4-perf with hard-matting, at anywhere from 1.66:1 to 1.85:1. For Super 35 films, the VFX would generally be framed with the intent of being vertically cropped to 2.35:1 for the anamorphic release prints. No matter how much additional vertical info might have shown up on the full-screen home video transfers, they would always be missing info on the sides.

(Not sure how much additional vertical info would show up on VFX shots in Super 35 films. Someone would have to compare the full-screen/widescreen versions of something like T2 or Star Trek VI.)

Side note: I've seen one film (or possibly a trailer?) that a letterboxed shot which was hard-matted in the camera, and actually had lens flaring which bled over into the black space! I wish I could remember what that movie was...