Yeah... those black trim pieces are not water tight.. they are cosmetic to cover over the fabrication and weld points in the body I believe.i like that better than the OEM.... but it is expensive... (you can use nets or tie down stuff thru the openings, you can not do that with the OEM's
IMO, that section can handle water, I don't think the strips are water tight either, it will just flow out towards the end of the car, and or evaporate.
Interestingly, in the new generation Accords... Honda finally figured out how to do the weld and bends on the roof top such that they don't need the trim pieces to cover weld points anymore... which is something I wish they had done on the gen5 CRV. Then again.. Honda probably figures a lot of people will just add rails anyway. The current generation Accords also feature an aluminum hood too.. which is also a nice refinement.