Update: This it was raining today. I realized I never reconnected the drainage tube in the bottom/side of the luggage compartment so I went outside to check. What I found was:
1) The bottom of the tube (blue arrow), disconnected from the valve that goes through the metal wall of the car and into the wheel well, was not wet and there was no water pooling in the bottom of the car. This tells me the water wasn’t reaching the end of the line so it must be kinked or plugged upstream. But remember, I successfully ran a nylon string trimmer cable through the entire tube and found no evidence of dirt clogging the tube.
2) the headliner was the wettest right around the hinge for the cargo access door (red arrow). I could see a drip falling from the metal directly above it, as well as a drip running from the same piece of metal to the left, behind the upper cargo side panel trim. If the leak were coming from the moon roof drain, I don’t understand why it would be so wet all the way back where it is.
Are there any other areas where water could enter on top of the car around the cargo door? The antenna for instance? It can’t be the door seal itself because the drip is above the door seal.
A leak in the back of the roof still wouldn’t explain the dry end of the tube tube in the lower side panel/floor trim…