Had a huge pool in my trunk after the rains this month as well. For me I think its the weather-stripping on the trunk. Both my taillights were immaculate when I check but the bottom of the trunk weather-stripping seemed to be bad and easily moved.
I guess those 2 black stopper things were suppose to allow water to leak out the bottom of the car if you remove it?? Engineers knew water was gonna get down here lol