I couldn't find much info about where the 5th Gen sunroof drains come out. I knew they came down the A pillars and somehow out the rear (Just like the 4th gens, there's one run through the tool area in the rear). My sunroof was holding water so I knew I had a clogged drain. Turns out it was 1 of 4 that was clogged the others seem to drain out of the pinch welds with no access to the "exit end" - Toyota this seems like a horrible idea.
My Front Driver drain was the one that was giving me issues so I spent a while trying to track it down. I had tried the weedeater string, and even a coated braided steel cable. It seemed to run the same length down each side before bottoming out so I wasn't sure what was causing the clog.
Once I stripped away some of the panels and electronics I pulled the hose out to find the small "filter plug" on the bottom. This is what was causing my tools to bottom out, and it's also what was causing the clog. Mine was packed full of debris. Figured I'd share a photo in case anyone else is having a problem tracking them down.