I don't think changing the exterior / inteiror color would actually cost more than changing the whole transmission.
Changing the transmission requires a lot more work to be done, where it involves the drivetrain, and I think thats something you don't want anybody to touch except Ferrari people.
Will you be buying the car new or used?
If you are buying it as a new car, Ferrari can do all these for you. You can pick any color exterior / interior, transmission, and even the materials used in the interiors, all at an additional price of course.
But personally I think it is the best way to do it, because everything is factory-built and it will have a better resell value.