Adam, it's explained a little ways up in the thread, and more eloquently than I could put it. I just thought that I would post this list because I think it was unclear just how many (and which) shots were affected. Sad.
skimmed the thread twice now (earlier and just now in more detail) and see nothing about cropping until your post, (I also did finds for "shot" and "crop", came up with nada) maybe the discussion was in another GWTW thread.
These shots were altered for the 1954 re-release, which was the first re-release in the widescreen era. It was determined that the movie as a whole played fairly well when cropped to a mild widescreen with the exception of these few shots. So, they were recomposed and reframed so that the theatre cropping would remove the black bar rather than any significant picture information. Trouble was, these shots were then inserted into the negative and the originals were presumably destroyed. The multiple generations of duping required to do all of this is why the shots themselves traditionally look muddier than the rest of the film, although they don't look too bad on the BluRay.