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Ah, thanks for these thoughtful explanations.
I had always thought such things would do it the way that git does it -- a note would be a unique thing, and then any revisions to the note -- the edit -- would be new things, determined by content-addressability, that could have some relationship to the original thing (e.g., a parent relation, a 'previous-version' relation, etc.) That would disambiguate what people are replying to.
But of course, I'm sure there are a billion nuances to it.