If they approved the work to be done, and the extra protection was in that estimate, then your golden. If its not, then you have an uphill battle.
The bodyshop, as david suggested, should be able to sort this out. All they need say is its included in every repair, or it was explained to the adjuster that it would be put on.
what it sounds like is they didnt know this special film was being applied, didnt know it would take a 30 day cure process, and you had a rental car for 72 days. They arent happy about that added cost. But as you explained even the 11 days wouldnt have worked considering the time it took to get parts.