Something you'd want the dealer to know is that you'll not take the car if the gear swap is going to cost you more than the factory install. This no doubt will make them match it if they want the sale.
Then again, the 2014 Mustang
orders are closing to an end soon. They may be able to sell the Mustang as is, so perhaps they will agree to walk you away from the deal.
it's all in how they want to treat you as a customer I'd think. If you have it on paper that they would allow changes to the order up to a certain date, and you made that date, then I'd say you will get the gear swap for the factory price.