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Why oh why can't I have the hatch (or the hatch glass) open and have all the interior lights off? This is possible on every other SUV i've owned. Hell, I can even do that on my 92 cherokee!
It has a door ajar switch in the latch for the window. Take the rear hatch panel off and unplug the ajar switch and see if that cures your problem. If it stays on then jump the wires to the switch. One way or the other it will make the system think the window is closed all the time. Then of course the rear wiper will always be functional when you do this so just make sure the wiper is in the off position when you open the hatch which should be no chore to remember for 99 percent of the population.
I will have to double check, but on my 01 EB there is a 3 position switch on the overhead light on the roof at the back tailgate. In one position the lights do not come on for hatch or window opening we used it at the drive In it looks to be factory original and part of the light bezel/housing.
scholzee is right, I had an 01 and now have an 04 and they both have the three position switch that will turn off the light if the rear hatch or window is left open. I have used the switch when hauling items that were too long to fit in rear with hatch closed.
The light switch must be a new feature in the '01+ models. I know there was no light switch in the '97 X we used to own.
Never tried it with just the glass, but with the entire rear door open I'd use a screwdriver to trip the latch making the truck 'think' the door was closed. Only issue is to make sure you lift the handle to unlatch the mechanism before trying to close the door.
You can take a large key ring, and shove it into the latch to turn the light off. Then, turn the handle like you are opening the glass, and pull the ring out. It works great for me, and it works on any of the doors.