This is far from the first time that coachbuilders have had window designs that do not match the door frames, or some other oddity to the body line, so this is nothing new. This does not look any worse than the strange window design of the 90s Federals that had no flow at all, or the 93-96 S&S/Superiors that the window was canted so much that you can never get the drapes to look even.
Yes, this one is messed up, but I have seen much worse.