The difference is that on actual HN, it takes more than one flag vote to hide a comment. (I suspect it's in the range 2-5, but I don't actually know.) So one person can't make a post they don't like disappear.
HN flagging is not meant to hide people you don't want to see reply to your comments, it is meant to identify rule-breaking comments.
I don't know, but I would suspect if the user who wrote the parent comment flags a reply, it would be less weight than if another random user flagged it.