My understanding is that in order to continue participating in the DMCA the recipient needs to act on all requests. That doesn't necessarily mean they need to take down the content, just that they need to respond to requests.
There is also no penalty setup within the DMCA for sending a request in which the response is that the content is not in violation. The only part of the DMCA that sets up penalties for the requester is if the requests are made in bad faith. That basically would require Microsoft to show the MPA is malicious in their requests rather than incompetent. That can be difficult to prove.
Hey! Finally a legal reason not to have massive centralization! OK my enthusiasm is exaggerated.
And the safe harbour provision only protects Github from hosting or referring people to infringing material, or material that's "subject to infringing activity" (which is different from what's being claimed here as nyaa is very clearly the object).
That said the DMCA contains all kinds of vague phrases, such as
> linking users to an online location containing [...] infringing activity
whatever the hell that may mean.