It depends on what you consider "proof". In or around 1983, my cousin (who posts frequently on this website) bought a 1968 GT Coupe, J-code with a C4 transmission. Car was out of Metuchen, early build date (Sept. 1967) and was built as a "Local Promotion" for some dealerships in and around the greater Newark, NJ area. So far, I have documented the existance of 3 of these cars, all with the exact same options including exterior color (Sunlit Gold) and interior trim (Black standard buckets). VINs were approximately 50 numbers apart, same build date.
I have the Marti report from the one that he owned (I bought it from him in 1986 and sold it in approximately 1991). Listed on the report is the 3.00 open axle ratio, which is listed on the option sheet of the report as an "optional axle ratio". When he bought the car, it was less engine. He installed a hot small block out of another car he owned at the time. That car also had 4.57 rear end gears (9"), which found their way into the coupe as well (just the center section, not the entire housing). It was a clapped out street racer, but very fast. There is no reason at all in my mind to doubt that the 9" housing in the coupe was the factory rear end housing. The standard rear end gear for the 1968 Mustang with GT equipment group was 3.25 open, presumably to give a little sportier performance for the car, being a GT and all. Hence, the 3.00 was listed as an optional axle ratio.
I can provide said Marti report for 2 of the Sunlit Gold cars as well as a window sticker from the third, all showing the optional axle ratio. I also have the email address of one of the current owners, who posts frequently on the VMF forum. He could certainly confirm the presence of a factory 9" rear end in his car.
Terry