Water inside rear hatch 2016 4Runner Ltd worried

Been loving my Forerunner but the other day after a heavy rain I lifted up my rear hatch and heard a swishing noise inside it. Was devastated and wondered how the heck did water get inside the hatch and will my electrical system now be eternally affected ? I drained the water out by pulling the inner hatch hand space out a little. The next day I took it to my dealer and they verified the passenger side drain opening was clogged. After a heavy rain today there was no swishing or obvious water inside the hatch. Still concerned though as how could Toyota engineer a hatch that would take on water internally especially with electric components inside the hatch. Dealer told me they tested it and it was fine but my concerns continue. Please advise. TY

 

When you change the air filter, poke the holes with a small stick-like tool. I used to incorporate this into my routine maintenance on an old Mustang that was notorious for it. Had an old Plymouth that had plugged drains for cowl. That was a mess.