The raw water spraying around the bilge from a faulty pump will cause a lot of rust that will look ugly and should be addressed immediately but shouldn’t impact the internal parts of the exhaust. Were the motors running hot? Were there any other symptoms? How did they diagnose the exhaust? Not sure how it would impact a transom assembly either. What is failing in the transom assembly? Is it attributable to galvanic corrosion? Sounds like you may want to get a second opinion. Regarding some of the other issues you described: I think it makes a good case for having a survey done on a brand new boat.