I have had the same water issue lately. What I did was to treat the gasket and hatch where it touches the gasket with Amour All to repel water trying to get in. I also sprayed the rubber grommets that shield wires at the top of the hatch. I used a thin blade screw driver to apply a small amount of silicone to seal the side window trim triangles on both sides at the top where it’s not visible when the hatch is closed. In the spare tire well I keep the rubber plug slightly ajar with tape to allow any water that get in to drain. This has worked well.
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