Special ordering items was very rare and salesmen would typically try and steering customers to more common combinations - sometimes to increase profits from my experience. If you wanted dual exhaust it was allot easier for a salesman to move you up to a GT or even take the single exhaust car to Midas once the car came in I've been told. Of course brochures and corporate documents always makes things look like its easy and a breeze when in day to day practice not everything works as planned.
Though we have always heard tons of claims from owners its has been my experience that almost all claims never have any supporting original documentation. Also consider somewhere these special things had to have a value/price associated with them for any order. Special paint was the easiest (price of the change was already determined) and most common in my experiences (having owned my fair share)
In many cases these "special requests" were instead handled after delivery by dealers.
The special order stuff when ordering a Ford seems much more common on commercial vehicles.
For passenger cars I sometimes wonder from some of the special order cars I've owned and seen if it was just not a slick way to get a hard to get model quicker than the rest of the dealerships.
Have owned more than eight special order cars - 65-69 over the years.
Just my experiences with the subject.
Would love to see an original Mustang order form with a special order other than paint or gearing.