As far as "Factory Option" versus "Dealer Accessory", here is what I can pass on :
1) The Tonneau Cover is shown as a Factory Option in the 1965,66 and 67 Mustang Sales Brochures (does not show up in the 1968).
2) The Tonneau Cover is not listed in the Salesman's Price Book for 1965,66 or 67.
3) The Tonneau Cover does not show up in the 1967 Showroom Factory Options Book (I do not have one of these for 1965 or 1966).
4) Thus, my "educated guess" is that if a Customer ordered it at the same time as they ordered the car, based on seeing it noted as an "Option" in the Sales Brochure, it was, most likely, actually installed as a Dealer Accessory (which, as Jeff noted, could have been either a "Genuine Ford Accessory, or an "Aftermarket "Accessory", depending on the Dealer and/or the Customer).
Bob