I don’t know about the JK doors, but the CJ doors that I have on my YJ are pretty heavy. And I can easily see where being hung by the window frame could damage the window seal.
I made a set of hangers for my doors using some scrap angle iron. I cut two pieces about 6” long, and in one side of the angle, drilled some holes so I could bolt the pieces to the wall in the garage. On the other side of the angle, I drilled holes that were just slightly larger than the hinge pins on the doors. With the two pieces of angle iron bolted to the wall, the doors just drop onto them just like they do on the hinges on the jeep.
I'll try to remember to get a picture of the hangers, and post them here.
maroon 1987 Grand Wagoneer. stock for now...