Yes. I got some weather stripping and stuffed it in those holes and then covered it with a black silicone sealant. Since I have a factory spray liner you can hardly notice my fix unless you are used to seeing daylight through those holes. It has worked out good for me. I still have a little leakage with my G4 Élite, but this cut down on A LOT of it. I have added some additional weather stripping on places where I could see light around the rails close to the cab. It's not perfect, but I live in PHX so rain in not my major concern, it is more the car wash run, and even then I always wash it when I am not hauling cargo back there so it will be dry by the time I need to use it.
But like a said a little weather stripping and silicone will seal those holes right up. I'll get a picture an post it up.
The passengers side had a bigger hole or gap on my bed to it took a little more weather stripping to fill the hole.