I'm far from an expert on this topic, and probably
few mechanics really could explain all scientifically. But I have heard that what you say is so. Can't imagine why this makes a difference, but it's free to mark things to replace them in the same orientation, so why not?
Balance is critical here with something potentially spinning at 6000 rpm, so I'd make sure the rebuild shop had good credentials with regard to balancing.
Are you sure there is a nut on the other side of the diff flange? Seems I recall seeing diff flanges that were tapped with threads.
Maybe spot an undercarriage shot in some DIY to confirm. Or look under your car.