Yes, there is a gap there. There is a slight gap around the back of the entire hardtop, but the one at the bottom of the quarter windows is the one you can notice the most. I've seen a number of these on cars and they all look about the same.
I have also heard that the rods are adjustable, but I haven't done it as I haven't had the need. If you find out the proper way to adjust these, let me know......