Flagging on HN isn't really the same as downvoting on Reddit.

From the HN guidelines:

If you think something is spam or offtopic, flag it by going to its page and clicking on the "flag" link. (Not all users will see this; there is a karma threshold.)

I think 27182818284 is talking about the downvoting of your comment, not the flagging of the original story.

Also, Reddit has the same guideline as you quote (only downvote things that don't belong) whereas HN has the creator saying that downvotes can be used to express disagreement.