That is an examples of GitHub allegedly violating the license of public repositories.

The claim that was made was that GitHub trained using private repositories and I have yet to see any evidence.

The caveat you missed in that case was that the person unchecked the checkbox that would allow GitHub to use files in his repository for training.

That caveat is irrelevant as it has nothing to do with a private repository. When code is public, especially with a GPL license, it can end up in multiple repositories which may not all de-check the share check.