To answer your question it was primer, undercoat, then exterior body color sprayed completely in the trunk.
Below are a few links of a concourse restored 69 Sportsroof. The trunk was body color but they did spray primer throughout the trunk plus sound deadner on the inside of the quaters and around the seams between the floor panels. The trunk's finished color would be the same as the exterior of the car. NOTE: splatter paint wasn't used in the trunks of Mustangs from the factory, I have seen many done that way but it's incorrect if you're going for originality. GM used splatter paint on thier cars though.
Limited Edition 600 Restoration - Part 16 Limited Edition 600 Restoration - Part 20
Shot of undercoating in the trunk in the middle of the page here,
Limited Edition 600 Restoration - Part 9
You might want to look through the car's complete restoration starting here,
Welcome to the Groovy Green Restoration Page
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1968 Mustang coupe, Acapulco Blue, 289 2v, C-4, Power Steering.
Hopefully a 1969 convertible or Sportsroof (non Mach or Boss) for next Mustang project
Trying to find my father's 1973 Mustang Grande he bought brand new. 3F04F126773 last known registration and title was in New Jersey, 1982.