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.
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.