I contacted Lionel's customer service mainly about the incorrect domes and got the sort of reply I expected:
"We apologize this is not as expected. We did check and this is how they are manufactured. We are not remaking the roof or shell to correct this difference."
The person answering did not even understand the product well enough to realize that the dome is a separate part not requiring a new "roof" or "shell".
Interestingly, the K-Line California Zephyr cars did the iconic Budd dome rather well. It's ironic that Lionel now has all the K-Line assets, but couldn't get the Blue Bird's dome right.