At my dealership, there were a few people that came in and ordered Mustang GTs exactly how they wanted them, the Mustangs arrived some time later and they took delivery for the same window price that they would have paid if it was just sitting on the lot. We don't charge more for that (nor "market adjust" the price of the Mustang as some dealers do, you pay MSRP at our shop); but that's not to say that all dealers are like that.
On a side note, we haven't had a single GT sit on the lot, they sell as soon as they come in. If we don't have one that is exactly what I want on the lot when I get mine, we are either going to dealer trade (preferably) or order one up to my liking.
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