This evening I decided to take another look at the wires going into the rear hatch. I had already cut open the boot several months ago and took a cursory look at the wires and thought they all looked good. Tonight I grabbed each wire individually and gave them each a solid tug and the large brown grounding wire came right out! So the ground from the body into the rear hatch has been completely broken. Explains a lot.

I removed some of the rear ceiling trim and moved the headliner back in order to access the termination block for the wires coming from the rear hatch. There is actually some slack in the wiring between the door and the termination block so I was able to pull the wires out a bit and find the other end of the broken ground wire. I temporarily spliced them together for testing purposes and now:

* The third brake light works as expected
* The door close assist works as it should
* The bulb-out indicator on the dash works now

I would prefer to repair the broken wire in the harness and reinforce some of the other wires without taking the harness completely out. If anyone has any suggestions on how to best do this I would appreciate it.