I don't know why FR lets this stuff out of the factories and I'm sure your unit was built in a different factory than mine. Same thing happened with our FW, duct work was "crushed" somewhere between the kitchen and bedroom. It came with only one AC in the rear and couldn't cool the BR in FL heat and humidity.
In all fairness, our dealer was great and their tech is the one who found the problem. FR's solution was to install a second AC in the BR at their cost. It seemed like a good idea at the time but it caused a build up of extreme condensation in a four foot area on the ceiling where the ducting wasn't letting air flow go by. So, don't let them do any more blocking of the ducting because you'll end up with mold/mildew problems somewhere down the road, after your warranty expires.
The real fix is to reverse the build and remove the roof, as you were told. We subsequently experienced some other serious problems. After a lot of negotiation, FR agreed to bring the FW back to the factory for the major repairs. We were in the 11th month of ownership at that point. They also agreed to extend our warranty an additional year. In the end, we decided we just didn't want to deal with FR and a unit we no longer trusted to go long term. However, FR has a reputation of really doing a good job with factory repairs, so my suggestion is to find the proper contact person at FR and start a dialogue.
--2005 F350 Superduty Crewcab, 6.0, 4wd, short bed, 3.73 gears;
--2016 Montana 3711FL, 40'
--2014 Wildcat 327CK, 38' SOLD