as far as "being given the option" the dealer will order what you tell them to order. But yea if your order is still "in processing" then you can add the 3.73 to the car
However esentially your order date for manufacturing purposes will then read from the day you made the updates rather than your original date so it could take longer for your car to be built.
2011 Mustang GT Premium
Rapid Spec 401A, Kona Blue, Brembo Package, 3.73 Rear Axle, Electronics package, GT Coupe pckg 5