My neighbor is with the CHP and this morning I ran into him as it was his day off. So I explained this "hypothetical" matter to him and asked his opinion.
He is also a car guy.
Without hesitation he said that if a car is hand-built with no VIN, then the State inspects it for safety, proper operation etc and can issue a VIN to the car if all proof (including receipts) is provided that it is truly a specially built vehicle. He said they do it with home made trailers all the time, but not too often with actual cars.
He also confirmed that the VIN (if present) has to go with the chassis. Similar to bringing in a re-bodied VW or Porsche, but the VIN HAS to match the chassis.
He said there is NO WAY I could roll in with a VIN on a custom built chassis without an MSO. When I asked him "what if it was a VIN from say, a Mustang" he said that as long as the whole chassis can be verified to be a Mustang it might work. Then he laughed and said that if it's some custom frame / chassis and has a Mustang VIN that's in the database and no MSO "Then you've got a real big problem".