Whether it's Jeep, Audi or any other car maker, it's really hard to keep a water tight seal on a roof that opens up. It's just the nature of the beast.
I know on my hardtop JK, there's a rain gutter like channel on the edge but water never came in after door opened. Then again, you could be right since I live in SoCal with the lack of rain we have, maybe that's why I dont have leaks problem.