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I think there were little rubber conical nubs that popped in there from the bottom. I'm not sure if many cars even came with them, or they all disintegrated over the years. I think it's a rattle deadener.
My Dad bought a 1970 Supreme in 1977 and those holes were empty. I vividly remember that detail after the first time I cracked the back of my head on that dang tongue. Sure woulda been nice if Olds had installed a rubber guard of some sort.
Its possible they were used to locate the part in a fixture when the holes for the different emblems were drilled. I have no proof, but its a possibility