I think they mean that these are internal github-org repos.

The ones used for running the site itself.

Though, its so many that i think there are some customer ones in there too.

No, there's no joke, you might have just misread the article (the 3,800 number is the number of internal GitHub repos the employee had downloaded on their personal computer / had access to on their own GitHub account)

The breach is about internal repositories, not user repositories.