I'd say that its more than likely a guide pin for initial soft top installation during production. It looks like its had plenty of use. It was probably left in there when someone went on break. You're either missing a fastener for your soft top, or they pulled that pin out and set it to the side and forgot it while they were installing the top. Make sure the driver side and passenger side rear attaching points have all the same fasteners in the same places and you should be good.
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