You want my 2 cents?
There is a difference of about 800 pounds in GCWR between the v6 with 3.92 vs v8 with 3.21.
If you've tried to tow with both, you'll immediately discard all tow ratings as "absolutely true and unfailable", because you cannot reduce towing down to a single number. The v6 will feel much weaker vs the v8, certainly much weaker than the 800 pounds suggests.
One of the tests they do in j2807 is 0 to 30 and 0 to 60. The 3.92 will launcher harder from a dead stop, no question, and thats why the 3000 pounds rating is increased. However, if you're on an on-ramp in third gear and need to WOT to get up to 60 mph and merge, both trucks will dig just as hard - or if you're on a freeway trying to pass a semi, again both trucks will be equivalent. The transmission just sits in one lower gear in the 3.21. Remember that you need to multiply transmission gear by axle gear to get your final gear ratio, so you can increase the gear in either spot to get identical torque multiplication; except when both trucks are stopped because then both transmissions are in first so the only play left is the one with the deeper rear axle (3.92).
I think you'll have a hard time finding reports of transmission or axle damage due to towing with either 3.21 or 3.92. I know that's the jist of your question, I wouldn't worry about it. Just treat your truck "normally", take off from a stop no harder than you need to, keep the RPMs above 2000, and you'll be fine towing loads < 8000 pounds. And if you want to tow more than that, you're kinda in the wrong truck anyway as you're going to hit payload and RAWR issues not to mention a soggy suspension.