I took a look at my truck and the top hole of first photo had nothing and the top hole of the 3 had a plastic wire holder, such as the ones used for the wiring harness that runs along the LH inner fender. I would think the next 2 would have the wire holder in them if you ran the wire differently. The hole in the 2nd photo has nothing in it. I'd say it was put there for some sort of accessory your truck doesn't have, most likely a bigger truck might.
