I've had water leaks from the tail light seals and from the black plastic seals along the top of the rear trim on the outside. Siliconed the crap out of all of it, and so far so good.
I did have one more leak. It's was a very small rust hole under the back bumper on the body that developed when I washed my car with a garden hose and punched right through the thin layer of rust.
I've also noticed that when you open the hatch on a rainy day, water likes to run off the corners of the rear glass, and drips right onto the plastic with the vent that protrudes in the trunk. That's another way those crevices like to fill with water. And from what I've seen on other cars, that's a notoriously bad spot for water to seep through the pinch welds and separate them.