If you take it to the factory and they do ANY changes to the structure, indicating that an error was made at the factory, I would guess that you have a good case for re-reimbursement, regardless of warranty expiration date. A mistake is a mistake and not readily uncovered during the VERY VERY short warranty period. Unless the windshield was out, NO inspection could uncover a hole that was cut too large or a flange that was not left large enough during construction.
I would insist on watching/filming the entire repair.