Would invite you to read the article in the Library under the 65 heading titled -Undercarriage - Finishes and Sealer Guide for 1965 San Jose Built Mustangs & Shelby's Also the detail has been addressed in a number of threads in other sections
Same basic details as for all San Jose built cars. Fenders were painted with a red oxide colored primer sealer (different from the undercarriage and often other bolt on parts) then the outer surface with a light grey primer surfacer. This along with the body color were applied with the fender not yet bolted to the car. The back side could have received direct paint from painting the fender lip, back edge and the headlight bucket applications since some of the back side of the fenders are in line with those surfaces and heavy to minimum overspray on other back side surfaces. At the other end of the range of possibilities was a decent coat of exterior paint if the painter get carried away.
Sound deadener, a little or more depending on car and pattern, was added much later after the car was pretty much finished and the fender was bolted on the car
Take a look at the article - it may make things easier to understand