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I agree. Most of my duplicates came from the raw disc files. I too dump some content to MKV (mainly TV episodes) but those files likely have much less duplication, though I do recall some of the duplicates coming from The Office in MKV.
(I do wonder if those The Office duplicates were something like the opening title, or scenes from the episode showing clips from previous episodes because it seems highly unlikely that the raw video streams were similar.)