I'm eventually going to get to mine, after I finally fit the top. I'm still going to move forward with aluminum ferrules epoxied right into the door top. They are very low-profile. Once installed they won't be obtrusive or very noticeable. How much do you notice the snaps for the tonneau? The ferrules don't stick up much at all.
Since the door top is angled TOWARD the window it isn't a big deal to bend the window's pins to the right angle. The pins will end up almost perfectly straight. The windows are angled top-in a little. It'll look fine and work fine.
Troy designed the pin system so that they can be fine-tuned to your particular car.