Here are some pictures, hopefully it will make it more clear...
You can see, the top of the door glass sits on top of the upper seal. The upper seal has two parts, one that is effectively over the door glass, and part of the same piece, but another section that is effectively over the rear quarter window.
The window sits at one point or another (usually towards the rear of the door glass, up top, but can hang as far forward as where the glass starts to slope down towards the front), and the seal presses the glass outboard. SInce the glass is structually held at the bottom, you get a small gap along the vertical edge, which I tried to get an image of.
I think it has as much to do with the upper window seals being hard and unforgiving as anything else. Ive put some lexon vinylex on them to help plasticize them a bit... we will see... Krytox grease would be my next try... replacement will need to occur at some point.