I think the problem is likely a combination of engineering misses. These trucks have a spoiler that water can get past in multiple places, a weak window frame that cracks, a poor job of sealing the glass to the frame, tabs and bolts that pass through to the inside of the cab, and a gap between the spoiler/glass/frame that allows water and gravity to do its thing.
My concern is that if you completely seal the bottom of the spoiler, the water that gets under it from the top and light will pool underneath. Then the path of least resistance takes the water through the tab and bolt holes. Not sealing the channel on top of the glass allows water to make it through the cracks and inside the truck, and it drips in along the rails inside.
That is my conundrum when thinking of solutions to the problem. The only full proof solution at this point is to get a solid window. The downside of that is it will affect trade in value, because I am effectively removing a factory option.