All I know is that the engineers didn't design them so the pinion hits the differential carrier.
Something has gone wrong on those that are marked up to reduce the clearance between the pinion and carrier. Wear in the pinion bearings, which would increase backlash as well as axial movement of the pinion, could easily account for the interference markings. That metal that used to be on the carrier had to go somewhere, and would increase the wear rate of everything.
If yours was checked out and cleared for use, then that's good.
