The 69 Road Runner hood stripes were definitely painted on AFTER the body color. I owned an original paint 69 that I bought from the original owner.it was coded for and still had it's original hood stripes. There was overspray under the hood on the cowl top and inner fenders because they did not mask underneath at all. The factory just masked off the outer and sprayed it. I still have the rt front fender from that car which clearly shows it.
Now on the 71 Duster with that total blackout on the hood, cowl and door top edge
( the cars with the huge 340 Wedge decal )it WAS painted on before the body color.
The 69 Road Runner bodies were baked after painting, then the stripes were done,so there was no risk of the lacquer attacking the paint