Last month I purchased a 2002 T4R 4x4 to pull behind my motorhome. (I had previously towed a 2000 manual transmission T4R 4x4 for over 75,000 miles with no problem. For the manual tranny, just put the transmission in neutral, leave the xfer case in H4, and tow away. But, age has finally overcome my desire to shift, so to an automatic I go.)
Anyway, there is no clear answer to your question regarding flat towing an automatic T4R. As you can see by the responses here you will get lots of guesses, but nothing definitive. For sure, Toyota definitely thinks you should NOT flat tow it and states so in their owner's manual (I think somebody already posted the quote). However, they do not tell you what might break. I have even called Toyota USA and they would not (could not?) tell me what might go wrong. So, I decided to risk towing my 2002. So far (about 1000 miles) no problem; but this is not enough miles to really test.
When towing, I put the transfer case in neutral and the transmission in park. I have no technical basis for putting the transmission in park - just a gut feeling that putting it in park will keep any parts from turning. Probably doesn't really matter.
Putting the xfer case in neutral does engage the ADD for the front axle. This means more "stuff" will be turning when you tow than when driving with the xfer case in high and the 4WD disengaged. However, the turning will stop at the xfer case. BTW, there is no clutch in the xfer case. Take a look at the service manual diagrams.
How far will I go before something explodes? It's anybody's guess. It's a gamble I'm willing to take.
I guess this is just an experiment in progress.
This does not answer your question, however.
Jim