I think some people are missing a major point about youtube-dl's takedown. The purpose of this DMCA claim wasn't just to prevent people from downloading videos, it was to set a legal precedent for the RIAA and similar organizations to troll Github and anyone hosting public repositories with it, by linking them to "illegal downloads".

By agreeing to this without any public opposition, Github has become similar to Youtube itself, in that it will be expected to immediately comply with à la carte takedown requests by RIAA and other copyright trolls from now on. It doesn't matter that the actual reason to take down your large repository is political or it simply bothers certain company for miscellaneous reasons, since all it takes is some "illegal content".

I am sorry...but what would the RIAA troll Github for exactly?

Github hosts tonnes of bittorrent clients - should those be taken down too? After all, bittorent can be used for downloading content illegally!

The supposed claim wasn’t that it could be used for piracy (despite many here parroting that claim), but that they advertise that it could be. I haven’t read the actual claim, but it seems they’re basing their argument on a block of test code that uses a video containing RIAA copyrighted music. It’s sketchy at best, but there’s a reason BitTorrent clients make no mention of piracy sites at all; The MPAA and RIAA are extremely litigious and will use any opportunity they get.

I'm not aware of any notices filed against that specific project.