Sounds like a vinyl top car with no vinyl. My 65 Landau has the same three big holes to mount the bar and the three smaller holes. They were most likely there when the sheet metal was stamped and Landau holes added later as that panel was altered for the Landau bars. No need to "fix" them as they would be covered with the vinyl top cover.
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2010 F150
2008 Shelby GT500
2005 50th Anniverary Edition Bird
1965 Special Landau
1960 2Dr Ranch Wagon
1957 2Dr Ranch Wagon
1957 Ranchero
1957 Retracable
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