Glad to hear that you found the leak.I have a Sienna 2001.
I've had the wet floor carpets for almost 2 years.
I have checked and rechecked all the doors rubber seals (weather stripping). There isn't a no sunroof.
I almost yanked out all the side plastic boards.
I just found the source of the leak last Sunday.
The REAR LIGHT (red) above the rear windshield had faulty rubber seals. The seals soaks water and allows water to drip into the inner boot lining. The water this seeps through the boot panel and flows under the carpet in the boot. With heavy rainfall/water it soaks the underlay and gets up the driver and front passenger foot-well.
I couldnt get a repalcement seal on a Sunday, I had to create a "gasket" replacement froma rubber carpet for the light assembly and ensured I screwed it on tight.
I yanked out the upper (inner) plastic of the boot door and the dripping I noticed earlier stopped when I poured water on the light assembly.
I hope this helps. View attachment 5538