I have the Rhino Racks (and I am talking about bars here, not a tray, however I am going to look at putting a tray on the bars) on my STX and I was also concerned about the water leakage (because I read about it here)
However I have had them on for 6 months now, not a drop of water inside yet.
The install instructions are pretty specific about where they go on the roof, with measurements etc, I wonder if those that are getting leakage do not have them in exactly the correct position? I am not sure, but I don't have any dramas.
Also they do not install into the holes, they just clamp on in the door seal. Possibly the difference? In my looking I did not see any that bolt into those holes, only clamps like these. The bars cost me about $300 if i recall correctly.