Hacker News Reader

Does not explain why there is any difference between a logged-in user and any other for reading.

Even on HN you have to be logged-in to see dead threads and comments.

You haven't really explained the reason.

I would guess this helps prevent spam by hiding the spam comments from bots that may index it. Indexing bots aren't usually logged in.

Indexing would have been my first thought as well, but since I don't work for neither HN or Github, any answer I'd give would be speculation.

That would be something that matters to github not to a repo owner. Why would that be a repo owner tool if that were the reason for it?

It doesn't add up.