That's what I was thinking. There is a consistency there that speaks to this being the case.
This does conflict with reports that Pacific Titles redid all the opticals using the original negative pieces. It also conflicts with the quality you can see yourself, as the 1997 SE wipes do not look as grainy as 20-year-old optical composites. In the Anatomy of the Dewback video feature, they even show the sandcrawler shot and how they totally re-did the wipe from scratch using new optical printers. They even showed it being done.
So, this doesn't make sense. It could be as Baronlando said that they didn't care or want to match the old wipe 100%. If it started a frame early, who cares. But the consistency with which this happens to "cover up" the old wipe is bafflingly coincidental if that is the case. Are there any exceptions to this that you have found?