64 Dart Hardtop Window Adjustment

I am replacing the window gasket/seals on my 64 Dart GT hardtop. Looking at the seal cross-section, there is an outer lip (exterior side), a center channel, and a static inner lip. In the factory technical manual for this car, it says to adjust the window glass so that the top edge of the window mates with the outer lip and pushes it slightly inward when the door is closed. That generally makes sense. However, when the window is rolled down, then back up, it naturally seats in the center channel. The rear quarter window also seats nicely in the inner channel. Are there meant to be two "modes" of sealing for the door glass: 1) mating against the outer lip when the door is closed, and 2) seated in the center channel when the window is rolled down/up without opening the door? Mode (1) causes the door window to be pushed out slightly from the quarter window, whereas mode (2) results in a good seal and both windows aligned properly. Any past experience, hints or recommendations would be appreciated!