The film was shot Academy and matted. Moonwalker was intended for theatrical release, but also for the song segments to be shown on TV as music videos. So it seems to have been shot to work in both ratios.
Usually, "open matte" home video transfers lose a tiny bit on the sides but gain more on the top and bottom. On the other hand, if the visual effects scenes are in VistaVision format, those scenes have a little bit of extra image on the top and bottom but lose a lot more on the sides. (Some examples: the Back to the Future trilogy, Who Framed Roger Rabbit, Honey, I Shrunk the Kids and Jurassic Park.)
Dream Quest did the effects for the Smooth Criminal/Mr. Big segment, and I believe they used VistaVision. If this is the case for Moonwalker, then any time there's a scene with optical effects in that section, it will be the widescreen version that has more picture info, not the full-frame.
That said, the zoomboxed-to-hell YouTube clip of Smooth Criminal sourced from the Moonwalker remaster is absolutely not representative of the actual framing of the Blu-ray release.
This is from the Blu-ray:
This is the same shot from the YouTube clip posted by "MJacksonHD":
So don't worry TylerDurden, the actual BD is not horrifically zoomboxed.
I don't think this "MJacksonHD" channel is officially sanctioned by Sony or the Jackson estate, either; it seems to be a fan. Whoever it is, the crop job is almost certainly theirs, and not an aspect of the BD transfer itself.
As to *why* that YT clip is so severely zoomed - you got me. Maybe it's some kind of trick to fool YouTube's copyright-infringement-detection-bots? I have no idea.