The sunroof has drain tubes that go from the A and B pillars all the way down to the bottom at the body seam to drain. My 4Runner had the rust in the same spot on the passenger side. Mine looked almost exactly like the photos. I cleaned it up pretty easily with some steel wool then put some cheap paint on it. Within a few months it came back. I need to clean it up again and put some high quality sealer, primer and paint on it. In my case it was coming from the outside, cause I was able to clean it up.
