There is never an extra fee for ordering a car from a dealership; if a dealer claims otherwise, you're getting screwed and should go someplace else.
Ordering has its advantages in that the car is exactly what you want, you'll know the price long before you get the car, and that it will not have been test-driven by who knows how many people. There can be (but not always) a bit of an advantage when it comes to negotiating price... the delare does not have the advantage of your emotion with the new vehicle sitting right outside waiting for you.
With the Mustang GT it will probably prove really weird (did I just say that?). Unless you have access to X-Plan or some other special discount, the best you can usually do on an 05 GT is MSRP (though a rare soul has gotten lucky). Most used 2005 GTs I have seen are selling for more than the sticker price of a new one. And from what I understand Ford is not taking any more orders for 2005's, instead saying that people would need to order 2006's. Heck, the 2005 GT may be a bit of a "collector" car, holding its vaule a bit better, because so few who wanted one could actually find one. Who knows?
That said, I think your best bet is order a 2006 when you can. The way the '05 is going, there won't be a drop in price in the next few months because the demand remains sky-high. Why but slightly used when brand new will likely cost the same?
Good luck with your choice...