It's really, really, really stupid, because it presumes guilt before innocence, standing in opposition to most general legal principles.
If anything, Microsoft via Github would do well to assert itself by not conforming, forcing the court to examine the DMCA's legality and process.
So shouldn't the next US-American recipient of one of these notices refuse to comply on the grounds that the law is unconstitutional?
The U.S. Court of Appeals for the Fourth Circuit in 2006 begins a discussion of possession with:
"That possession is nine-tenths of the law is a truism hardly bearing repetition. Statements to this effect have existed almost as long as the common law itself."
Willcox v. Stroup, 467 F.3d 409, 412 (4th Cir. 2006).
It doesn’t mean whoever possesses something is automatically the owner. It means that absent evidence of superior title, possession generally suffices to show ownership.