I don't play 12 string guitar, but on the mandolin, there is the 'Lost John' tuning where the 2 E strings are retuned to D and A, and the G strings are retuned to A and F#. The A and D strings are not retuned. This would be an example where the double strung notes are tuned so that they do vary significantly in the notes.

Is the 12 string guitar ever retuned in a similar way? Just wondering ...    -btmp