Each machine is calibrated at the factory so I suspect that that discrepancy is already accounted for. Also, 1/16" sounds pretty extreme, it actually sounds like they didn’t have the tray in the divots or that there was some other mistake in measuring.
Almost everyone’s tray height (tray, not lip) is right around 1.35.
How to properly measure tray height:
I’d be curious whether applying that technique to both machines – being very sure that the tray is properly seated – would yield 0.0625" difference in measured height.