The plastic tray should have a little gap between it and the body that lets water run off. I got replacement attachment pushpins, removed the pushpins, removed the plastic tray, and cleaned a ton of crap out from between it and the actual metal of the body itself (like, 20 year old decomposed leaf sludge and dirt). Then, put silicone grease around all the pushpin holes (they go STRAIGHT INTO THE TRUNK) and put the tray back. Water mostly quit pooling after that. There were no visible drains, either- it just kind of runs off the back of the car.
I've found like 6 or 7 points where water leaks into the trunk (just bought a neglected w215), so I suggest taking all the paneling out before it rains, and looking everything over. If water gets onto the electronics in the trunk you're gonna have a different headache.