the problem is when the safe-harbour entity doesn't actually try to protect their content creators, but blindly accepts any takedown. Youtube is notoriously obedient - to the point where it can threaten content creator's livelihood (see https://www.youtube.com/watch?v=QfgoDDh4kE0 for a famous one).
Doesn't matter - they have to accept the requests and sort it out later to retain safe harbor. That's just the way the law was set up. The whole point is that they claim neutrality - they are the carrier of the information, not screeners or judges of it. The legal back and forth is between the the entity posting the content and the entity submitting the DMCA takedown. After the fact, YouTube to Github can and should and sometimes do help fight back against abuse.
