Body Plugs for Trunk (71 Demon)
Looks like the holes from a trunk channel mounted radio or CB antenna.
Since you've already got it nicely painted, I would just go to the hardware store or electrical supply house and get some appropriately sized rubber hole plugs, installed with a dab of silicone on the bottom.
If you can't find that, a small pan head machine screw and nut with a rubber or fiber washer should do the trick.