So an update on this. I though it was probably the lift gate seal that was leaking, but upon further inspection I think I may have been getting the slightest water intrusion from a trim clip. When I removed the interior lift gate trim piece, I saw some water stains coming out of a trim clip hole in the body:
Looking at the trim clip for this hole, I noticed the little black washer was missing. Most of the others had it. I did pull this trim cover off about a year ago to replace the lift gate speakers and I guess I didn't notice that the black washer either ripped off or possibly stuck to the body and then fell off.
And Toyota calls this a "trim clip with sealer", so I'm guessing that little black washer is pretty important to seal out any water that may leak into the gate at the rear window.
So I'm assuming that a tiny amount of water slipped through this hole during heavy rains, and leaked down inside the lift gate seal, and caused the rust. I replaced all the trim clips without the black washer (3). I'm sending the gate seal back, and hoping this fixes the issue.
A better pic of which hole it was. It was on the right side.