it seems that the footage for the new docu has the footage sourced from the Warner DVD but in HD. The color timing is identical but the smoking gun is the screenshots with the same exact visual debris found on frames of the DVD version.
Now I'm not sure what exactly the source for the Warner DVD was, but it was promlematic in some areas (Showdown, Eleventh Hour, and some others I can't quite recall, have areas of the film which are heavily scratched, followed by a black frame. Most affected is The Bulleteers which had a second or two of animation not shown due to this). Evidently Warner thought it was worth it to go back to the negs for this one.