If I recall correctly, most dealerships won't actually charge you that much more to custom-order a car, because the car won't be sitting on their lot for very long compared to the cars they have to keep in stock and hope they sell.
You're referring to the dealership's working line of credit, which is just interest they pay monthly from time of vehicle delivery to sale. For most vehicles, this amount is negligible (unless its been sitting on the lot for months). You could theoretically get a deal on a car they can't move, but the long-term resale value will likely be lower because its an undesired model/color/etc.
And also the cost of the space taken by the car.