I scanned the replies rather quickly, so sorry if I am repeating what someone else said, but... My dd3 is not "one of those", but she certainly has her moments. And we (DH and I) want to walk close to the edge of what's socially acceptable, because we think it's great that she's analytical and detail-oriented, that she can articulate her reasoning, and that she is willing to question authority. But, of course, there are limits. And like you mentioned, TONE is a big one. And dd3 has got that concept down. Most of the time, if she's rude -- but right -- all I have to say is "Tone" or "Try again" or just give her "the look" and she'll say "Sorry," and then make her point in a polite way.
What I did was repeat what she would say -- HOW she would say it -- and then model the correct way to say thing. And explain to her about mutual respect, being kind, etc, etc. (And, of course, we do a bunch of stuff with tone when we read books; she got the concept that there are different types of tone down long before we did this -- but then she got the concept of rude vs. polite)
Like I said, dd isn't like your ds, so I don't know how helpful my experience is, but -- to reply to one aspect of your original post -- yup, a li'l one can get the point of tone. HTH...