If people get downvoted for posting a new reply to make sure the questioner gets alerted

Once again, you miss the point. You didn't get downvoted just because you posted a new reply, you got downvoted because your reply didn't add anything to the discussion. Simply posting a link to another site, without even a description of why, is both asinine and pointless.

then there should be an option to alert someone of a significant node update so he won't miss it

A "significant update" should almost always result in a new post. Adding a single off-site link is not significant.

Currently, the best way to handle a small but significant update is to both append the original post and create a new one, which is what I did. Appending the original will help people who've bookmarked it, and the new post will alert people who are just reading new replies.

I agree 100%, but again I reiterate that your example update was not significant. New posts containing actual significant information don't get downvoted, so your concerns are baseless.