I saw your suggestions as three separate recommendations rather than a package and was replying to 3) specifically.
the new reply could be attached to the parent of the comment that was written by the person who wouldn't see it.
I was assuming that the reply to the person would not be viewed by him if it was below his threshold, and also assumed that that person, like me, seldom revisits the thread unless a comment I have made is replied to or moderated, and thus wouldn't see it if I posted it elsewhere in the thread.
Of course, now that I think on it (having received notification of your reply), If I understand correctly, the system would tell him I replied and allow him to view it even if it was below his threshold. So there's that part of it pointless and dusted.
The part about the average threshold might still be useful, though--Consider if your warning said,
"Not only will the person to whom you are replying not see your comment, neither will [50% (or 75% or whatever)] of current readers."
"You are posting at [-1]. [60%] of our readers will not see your comment."
It might make the trolls think--or not.
-of course, I'm interested in stats like that, so I wouldn't mind seeing that posted at the top of each thread page, just to satisfy my idle curiosity...