I think I see what you are measuring. It's not the glass - it's the metal (red) parts between the roof and the liftgate, right?
I will measure all of the gaps on mine when I get it back - hopefully Friday.
Edit: I forgot. There is one more mis-alignment that my son-in-law pointed out. The rear plastic bumper cover isn't perfectly aligned with the driver's side rear quarter panel. The bumper cover sticks out a millimeter or maybe 2. Small enough that I didn't care (see my earlier post about my Chevy).