I have the exact same model truck with the factory spray-in bedliner. I decided on the Bakflip G2. Went on perfectly using the factory installed bed rails - no modification needed. Low profile, easy to access yet secure. I barely have any water when it rains. Only some wetness around the tailgate if it's a heavy rain. I recommend it.
Bakflip G2 tonneau, Factory spray-in bed liner, Flowmaster 50, Bilstein 5100's, Upper Glovebox Add, Tow Hook Add, Husky X-act Floor Liners, ProComp Wheels with BFG KO2's