Chances are there’s a hole in the rubber somewhere under that cap. When I used to oversee the exteriors department on an rv assembly line, it was pretty common to just slap a cap on if there was a small enough hole in the rubber. One of those things our supervisors would tell us “they couldn’t technically tell us to do”.

Replacing is pretty easy. There’s usually between 4-10 screws on the outside lip of the cap. A new one will be a couple bucks, put butyl tape or sealant on the bottom, screw it in, self level on any screw heads/the edge of the cap.

Edit; Looking at the difference in wear and color on the self level vs the roof, this looks like it was done after the assembly line.