I dunno.. I think I'm actually with Conley on this one, right or wrong. If a certain portion of a certain take was the best one but still needed a little Melodyne work, I would make those edits in-place and then bounce the clip, since I'm still (more or less) in the comping process. Then I'd flatten the comp using all of the desired clips, including the bounced MD version, and move on.
I guess an alternative would be to flatten the comp first, split out the portion that needs MD, and then do the Edit > Bounce sequence... without ever opening take lanes to see where that clip was located.
Moving the clip to a separate track probably is the
safest option, but it seems like a bit of overkill for a single "corrected" clip/take. Then there's shared plugin processing, sends, etc, etc.