> The rules in section 512 do not apply.
Assuming you're referring only to the §1201 'anticircumvention' portion of the claim (the main focus of the GitHub post), whether this portion is also subject to §512 rules is a little more ambiguous. §1201 defines a trafficking violation separate from copyright infringement itself, but some court rulings have established a requirement that §1201 violations establish a 'nexus' to copyright infringement in order to be valid. If this requirement holds, §512 safe harbor protections could indirectly cover §1201 claims as well. However, because there's a circuit split on the issue, unless GitHub is sued on this exact point it's impossible to say for sure what rules would apply in this specific case.
In any case, GitHub handled the 1201 takedown claim in reference to its established, documented process in handling takedown notices and counter notices [1], except for the fact that it didn't wait 10-14 days after receiving a counter notice before re-enabling this content. The deviation from their published policy is still itself noteworthy.
[1] https://docs.github.com/en/free-pro-team@latest/github/site-...