Ran into a similar situation when I replaced all of the weather stripping on my convertible. There are 3 rails on each side that hold the rubber and the factory used a variety of screws to mount them to the frame. I was prepared for this after reading a few DIY articles that talked about the inconsistency and how important it was to keep track of which screw went to it's original hole.
Maybe the same GM crew installed the rocker covers and the convertible tops?

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