I am not entirely convinced that the hard rubber screw caps were intended to be part of a finished car. I find no documentation on what to use and where. Yet they exist. I have not found a Ford part number nor installation instruction in the Mustang Assembly Manuals, the MPC or Ford Service Manuals.
Instead, I believe they were a "safety item" used to protect the hands of assembly line workers while the grills and upper deflector were installed, and the caps were left on the screw tips. Take a look in the area between the radiator support and grill on the left hand side of a 64 to 66 Mustang. There is nothing there to service, and no reason for an owner to stick their hand in that area, at least in normal daily operation. So why are they there? It may have been more expensive to remove the caps and reuse them than their cost.
Just a thought.
Jim