I'm a little confused here. The initial takedown request was from a law-enforcement entity in the UK, citing UK law: "Copyright, Design & Patents Act 1988, Offences under the Fraud Act 2006 and Conspiracy to Defraud".
And yet the repo owner was able to use a DMCA counternotice (a US thing) to restore the site? That... doesn't really make sense? Why would GitHub honor a DMCA counternotice when the takedown was not the result of a DMCA takedown request?
I do wonder if GitHub has opened themselves up to legal liability in the UK because of this (where I presume they, or Microsoft, have business entities). Either that, or this article is getting some of the facts or details wrong.