The ~140 MB zip file containing the code itself (but not the commit message) is still downloadable from the Wayback Machine, as linked from this comment: https://news.ycombinator.com/item?id=24996616.
Apart from the code linked above, I don’t think you’re missing any significant information that was on that archived page whose URL is now excluded. The screenshot at the top of this article matches what I remember of that page: https://arstechnica.com/information-technology/2020/11/githu....
To describe the screenshot in words, for the sake of those who prefer text to images for whatever reason: the commit was an orphan with no parent; it had no commit history. The message was as SethTro quoted it: “felt cute, might put gh source code on dmca repo now idk”. GitHub’s interface suggested the committer was https://github.com/nat, but there was no “Verified” label. The interface described the commit as having been created “1 hour ago” at 2020-11-04 05:00:26, the time of crawling.
I remember reading somewhere that once You include some url in robots.txt archive.org even though can have it archived it will stop showing it to the public.
The first page you linked tells the story of how the Wayback Machine once deleted archived content if robots.txt directed it to, but was moving towards not doing that anymore. You can also see in GitHub’s robots.txt that URLs matching `/*/tree/` should already have been forbidden, yet the Wayback Machine at one point had https://github.com/github/dmca/tree/565ece486c7c1652754d7b6d... archived. These facts suggest that it is your second theory that is correct—GitHub contacted archive.org to get the archive taken down.
This URL has been excluded from the Wayback Machine."