I use them for Github's `gh-pages` branches. However, the [official documentation](https://help.github.com/articles/creating-project-pages-usin...) suggests to branch of master and delete everything.
I also work in [a repo with three roots](https://github.com/libfirm/libfirm). It was different repos, which got merged later.
Yes, that make sense. An orphan branch is a nice way to bring in the disparate history of a separate repo that you've decided to merge into your main repo.