Remember the XJ as delivered by the factory has to work in north America. Then engineers have to take in the southern tips of FL and TX along with the north slope of Alaska when they design a vehicle.
They also say in my owner's manual that I can tow up to 2000 lbs without an aux transmission cooler. The Aux cooler is only required for towing the larger loads.
The stock configuration has the fluid going trans-rad cooler-aux cooler-trans. As we were discussing yesterday about what temp the aux fan comes on for a Renix XJ. The fan comes on in my 88 XJ when the coolant in the "cold" tank reaches 190F. So that tells us the coolant returning to the engine can be 190F or higher when the engine working hard.
In the stock configuration with the aux cooler the AFT can be leaving the rad cooler at 190F then go to the aux cooler which is say in a stream of 100F air. The ATF cools to some temp between 190 and 100F.
In the reverse routing you are suggesting the AFT would be cooled to a temp between the operating temp of the trans and 100F. Lets say it 150F, then it is routed into the rad cooler and that coolant is still over 190F because the electric fan is running on my 88 XJ. The AFT could be heated up to 190F then returned to the transmission.
I think the stock configuration is the way to stay. I do have a question for you, I notice on your signiture line you have 4.54 gears in the axles. The AW4 came with 3.55 gears and if you radio up tire sizes from a P215/75R15 (27.8 inch dia) to a 32x11.50R15 (31.7 inch dia) the gear ratio to maintain engine RPM at the same vehicle speed would be 4.05 gear ratio.
It sounds like you geared your XJ for 35x12.50R15 tires (34.7 inch diameter). If you had the 35s on there the calculated gear ratio would be 4.43.
Part of the problem could be your engine speed, you have too low a gear ratio for the tires you are sporting. The engine operating on the back side of the torque curve that why you are seeing the temp gauge results when you tow.
I believe I read on her in the past the top of the torque curve is 2400 RPM and the engine should be at the RPM or a couple hundred lower for your cruising speed.
Sounds like a perfect excuse to switch to 35 inch tires
If you're married you tell her "these larger tires will improve gas mileage and the engine will run cooler"!!!