1200 Mi Svc & "Transportation Mode" aren't related
The shop foreman may have been confused. In transportation mode almost all electronic systems except those necessary to start and drive the car are deactivated. You can think of it as a modified "limp home mode." They're activated or reactivated at the VDC (or VPC as it's also been called). The software change at the 1,200 mile service is unrelated to the transportation mode. I don't know what the specific software changes are at the 1,200 mile sevice but I've been told that the engine performance changes are relatively minor.