What we call DMCA takedowns, coloquially, with the whole counter notification process etc, are notices submitted under Title II. That title deals with copyright infringement, not anti-circumvention.

That means treating such notices as a typical DMCA notice, as GitHub has done, is incorrect. GitHub may well choose to follow the takedown if it considers it valid and the repo infringing, but what they've done is treat it as a copyright takedown. And that is clearly, unambiguously wrong, as it goes against their own DMCA policy, linked from the youtube-dl repo's disabled notice, which says:

> The DMCA notice and takedown process should be used only for complaints about copyright infringement. Notices sent through our DMCA process must identify copyrighted work or works that are allegedly being infringed.

So yes, GitHub messed up here. That doesn't mean they shouldn't have taken down youtube-dl, but they way they went about doing it is wrong.

You'll notice that the EFF, in that article, never goes into the details of the takedown process that happened. They never said what GitHub did was proper. They are just talking about the anti-circumvention law in general.