The safe harbor under Section 512 applies to takedown requests for content copyrighted by the person issuing the notice. I don't think there is anybody asserting that the RIAA is the author of youtube-dl and thereby eligible to make a claim under that section.

I would also be curious to see you cite a case that says that refusing a takedown notice in one case costs anyone the Section 512 safe harbor in all other cases where they continue to execute takedown notices, since that would be oppressive and ridiculous.