Upon further inspection, it's flush everwhere except the top right corner opposite the hinges. I can push it in a bit and then it sits flush, but then when I let off the pressure it goes back to how it was.
I'll add this to my list of things for my dealer to work on when I finally take it in.
I just took the Jeep to the dealer for this (and some other issues) today. When I pointed out some of the other issues he already was trying to lower my expectations by saying things like "it can't be perfect" and "they're built by machines not by hand" so we'll see what happens, but my fingers are crossed.