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".
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".