So my best guess is that even though the validator succeeds, the actual submission is pulling the GitHub page for the well-known instead of its raw content. The problem is you also can't really fix this yourself: The raw file is hosted at raw.githubusercontent.com which wouldn't match your source URL.

Hopefully they will fix their submission tool. I did see one project submitted successfully by having domain.com/github point to their project URL, which the submission accepted, but that causes certificate errors.