I've got an issue with our 2010 hard top right in that spot. When it rains, a little tiny bit of water leaks in on the door from that spot. Right on the freedom top panes, there's some spongy black foam where the panels touch the rubber door seals. The problem is that the spongy black foam is exposed to the outside, and then also extends inside the vehicle about 1/4 inch. When it rains, the part outside gets wet, and then through capillary action, the water soaks the part that's inside the vehicle (even though the foam is pinched by the door seal). The water then drips through the foam and into the car.
I'm going to fix it by trimming the black foam so that it doesn't extend inside the car. Seems like a silly design.