I noticed that as well. I'm certain that they can still be removed if I decide to add the lighting.you could get some caps at your local hardware store. Looks line they line-x over the pop outs for the bedlights too.
He's attempting to fill bed liner, it'll stick, my last truck was the 2017 RaptorThere are threads on the Ford forum about what you can and can't use on an aluminum bed, you can't use regular RTV if its in contact with the metal.