What considerations beyond costs should be considered

What considerations beyond costs should be considered when deciding whether to take a special order? Why does a company like General Motors allow you to "special order" from the "menu" but you can't have "off-menu" substitutions...you can order a blue car with beige or grey interior, but you cannot order it with the red interior that is available in a black car? Is there ever a time it would make sense to allow such an order? If so, how would you know what to charge?