Unfortunately, catalog copy outweighs a phone call with one individual.
Had Lionel put up a prototype photo of the Ferdinand Magellan in the catalog (or heavily photoshopped the model photo,) then released the car as it is, I would say there would be a case. But, there was no mention in the catalog hard copy or online the car was going to emulate the prototype. The car was produced as cataloged. There is no case here.
We're not dealing with Athearn Genesis, Rapido Trains, Scale Trains or Walthers here. We're dealing with the red-haired stepchild of Lionel and expectations should be lowered accordingly.
I suspect most of the Flyer Folks don't really care if the model matches the prototype. Had a new roof been applied, I would wager Lionel would have taken heat "because the roof doesn't match the other cars."