I had noticed about a year-and-a-half ago that every post by Popcorn Mariachi (creator of rapidsearch and therefore the archivist in your theory) was missing from the archive. This was strange to me because Popcorn Mariachi was the unquestionable king of /r/ from 2005-2008, being probably one of the most well-known/beloved tripfags on the entire site, second only to moot probably. As stated by Lurkmore, Popcorn Mariachi was "commonly seen as the patron saint of /r/ by most oldfags, Popcorn Mariachi is considered to be one of the best tripfags 4chan has seen, period." There is a considerable collection of memes and screenshots of Popcorn on Macrochan, further showing how embedded in the community he was.
The strangest thing occurs when you try to search for any of the postnumbers shown in the screenshots available or if you search for his name and tripcode on old.sage.moe: Nothing. The most damning evidence of automated and deliberate removal of all instances of Popcorn Mariachi and all threads they were posted in is the fact that not all instances of "Popcorn Mariachi" as a username and "!9i78bPeIxI" as a tripcode (his tripcode as seen in the screenshots) were removed, only those that had both, therefore only the real posts by Popcorn. Other posts by impersonators were not removed, seen here and here. This clearly shows selective removal, and this absence is not only on /r/ but can be seen archive-wide, on every board.
There are several other factors to be considered as well, such as Rapidsearch shutting down 3-4 months prior to the discontinuation of the archive (which represented Popcorn struggling to decide whether to actually go through with the decision to leave 4chan and the rapidsearch project forever) and the fact that the archive just so happened to end the day before /b/ reached 100 million posts, likely a milestone meaningful to Popcorn enough to cap off the archive. I haven't done a definitive search of Rapidsearch on the Wayback Machine yet, but one smoking gun in the FAQ section states "I was planning to have a feature where you could view the original post the rapidshare was from, but I haven't gotten around to implementing it (And uploading that much HTML would be not so easy on my slow connection)." The reason for the donation of the archive to Jason Scott would have been because Popcorn did not want all of his years of effort to be for nothing, and he requested anonymity because he wanted to distance himself from 4chan, wanting all evidence of his existence on the site removed.