I'm pretty sure GitHub does use alternates in the same way that that GitLab does:
https://docs.gitlab.com/ee/development/git_object_deduplicat...
I vaguely recall seeing @peff comment about this on HN years ago but I can't find that comment now. Here's a GitLab employee claiming GitHub uses alternates:
https://news.ycombinator.com/item?id=22179208
The thing is, that both the dmca repo and its forks must have alternates files to the same underlying common repo, otherwise the PR ref in the dmca repo wouldn't be able to see the merge commit pushed to the fork. Pushing the merge must have duplicated all the youtube-dl commits into the common repo used by both the dmca repo and its forks because youtube-dl and dmca would have different common repos.