Yes water can get between the liner and the bed, but if the gap at bed bottom and the header is clear, it lets the water drain out. Noticed that happening just the other day on my '06 F-150. Also, if water does get in there, it should flow out the back by the tailgate whenever you drive away. With the shape of the fluted ribs on the flooring, they not only add stregth but allow water to escape. As a matter of fact, I cannot drive away slow enough and not have the water exit out the back. I've been driving pickups for over 25 years and have seen everything that can happen in the bed of a truck.
