On mine, there is (and needs to be) Dicor (it could as well be Eternabond, but I happen to have Dicor) to seal the flange of the vent to the rubber roof. The tabs for the vent covers are raised a bit above the Dicor, and the vent cover on them. This does leave a little gap between the cover and the roof that lets pine needles in to collect on the screen in the vent.
The vent covers are well worth having. I would not have an RV without them, unless perchance it did not have skylight vents to cover for some reason.