They are referring to origin as the forked repository. E.g. if I contribute to nixpkgs (the NixOS package repository), I only have to fork it once, use that as my origin, and can create branches and submit PRs.
So, you are both right. If you contribute many times to the same repo, you only have to fork once. If you do a lot of drive-by contributions, you'll end up forking a lot of repositories.
(I fully agree that GitHub has a lot of overhead compared to git format-patch/diff. GitHub et al. also have some benefits in terms of communication. At any rate, diff/format-patch are not that hard, so I think any git user should learn it.)