I don't think that's a reasonable guess, and here's why: Yes, the FPC lists only one part number for each of the door shells, each of the door repair panels, the left and right front fenders, the rear quarter repair panels, the roof repair panels, and the trunk lid, per type of car. That is: there's only one left front door shell for all 4-door '65 Darts and Valiants. There's only one right front fender for all '65 Darts. There's only one trunk lid for all '65 Darts. There's only one left quarter repair panel for all '65 Dart 2-door hardtops, only one for all '65 Dart 2-door sedans, only one for all '65 Dart 4-doors, only one for all '65 Dart wagons. Only one roof repair panel for all '65 Darts except wagons, only one for all '65 Valiants except Barracuda and wagon, only one for all '65 Dart and Valiant wagons. And so on. Each of these parts would have different trim applied depending on whether the car was a Valiant V-100, Valiant V-200, Valiant Signet, Dart 170, Dart 270, or Dart GT. In some cases, the holes not needed for a particular car would be invisible behind that car's trim -- such as the holes for the trunk lid "D O D G E" letters on a Dart 170/270 being covered by the trim panel on a Dart GT. But in other cases, the holes not needed for a particular car would be exposed and visible -- such as the holes for the trunk lid "D O D G E" letters on a Dart GT being unused and exposed on a Dart 170/270. No way would that fly, having unused exposed holes like that. Definitely not the way it was done.
I think my guess is more reasonable: At the factory, the trunk lid for any given car was drilled only for the trim that would go on that car. Service replacement trunk lids were to be drilled by the installer. And a used trunk lid with unneeded holes that would be invisible once the car's trim was in placesuch as a 170/270 trunk lid being installed on a GTmight very well have had random tape applied by whoever was doing the repair work on the car in 1970 or 1980 or 1990 or whenever it was done.