If I get a chance, I'll send Dynojet another e-mail. All I know is...on all the dyno runs I've done (on a Dynojet) there is a variance if you are running anything other than 1:1, since AFAIK the dyno is calibrated at a 1:1 ratio. Otherwise, why not always just do them in 2nd or 3rd...since the MPH you reach in those gears (55MPH+) are all you'd ever seen on the road.
I wish I could find a dyno sheet of a turbo diesel....I've seen one where same truck, same dyno, same session the TQ was 200+ TQ difference just by using a different gear. And surely that's not from any drivetrain loss. But again...turbos can behave a bit differently on the dyno.