The only leak occurs when I go through a car wash. Their high pressure spray causes a slight leak at the rear full window lid/door on the driver side. Not sure, but a framed door may not leak there because it is more rigid. It has never leaked hard rain, only the car wash.
I did not order the rack, it came as a surprise (dealer error, no charge). Have never used it. A nice Thule rack. The cross members are key locked and removable.
I always order the front window with a slider window and to be detachable. Don't use it often but is handy for cleaning truck rear window. Best is, I can open the shell slider and truck slider to fit long items into the cab. I learned it's easier to have the shell slider open from/through the truck slider. That way, I don't have to crawl into the bed to open the shell slider.
If you have a dog that rides in the bed (mine rides in the cab), Leer has a great screen guard that mounts on the interior of the shell windows, allowing the window to be opened and keeping the dog inside.