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To answer my own question: I suspect SuperDuper is simply not designed for this type of operation. I've been playing around with AASync more recently, which is much more oriented towards basic user files, and can happily do a 'newer' style copy of user folders etc from the external HD to the comp's internal one.
Of course, if I'm wrong and SuperDuper can do the above without running from the external drive then someone please let me know.
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