In this case, the author did submit a DMCA takedown request, but the Github user then submitted a DMCA counter notification stating that, under penalty of perjury, they have a good faith believe that the takedown is invalid

Are we sure of that? GitHub publishes the notices and counter-notices. I can't find any notices there that appear to be for that repository, nor any relevant counter-notices.

I wonder if the author may have sent his request through some other channel than GitHub's DMCA takedown request form?