I think you must have misunderstood something. You can email hn@ycombinator.com and make the case some article or another does not belong on the front page (not original source, a dupe, linkbait, offtopic, whatever). If you're right, that article will be downranked, sometimes right off the front page. People do this all the time. It's the inverse of emailing to make the case something is misflagged.

What is true is that almost all [flagged] and [flagged][dead] is from user flags. But that doesn't mean that the only story moderation by moderators is just unflagging.