After some thought and a discussion with the body shop I have used for years when I need one, I did seal the top of my rear window with some flowable caulk. The truck was out of the 3 year warranty when I did it. Then shortly after, I saw where the warranty was extended for this problem for some of the earlier truck builds. Still the extra step gave me some peace of mind and it stopped some wind noise I could not pin point. That fact reinforced the choice I made.
What I do think is that because we have 4 coil springs, the frame flexes a little more than a truck with leaf springs on the back. Depending on how and where you use your truck that flex may contribute to some of the leaking problem with the rear window. My brake light did leak, which was replaced under warranty.
Just my thoughts on the matter.