I haad a similar problem, No visible water leaks from above, but 3-4 inches of water would appear in the spare tire well. It turns out that some minor body work had been done on the right rear quarter panel after a slight fender bender that happened before I bought the car. Well, they had fixed the visible damage but didn’t touch the inner piece of sheet metal. The inner piece had been bent where the plastic exit air vent is and when driving through water, water would splash up to the inner panel, run down and enter the trunk throuth the space between the bent panel and the top of the plastic vent. I straightened the panel and I have had no trunk moisture since then (over 1 year).