As far as I know, there is no standard for tow ratings, so manufacturers basically get to make up their own based on what they feel will not lead to warranty claims and/or law suites... So, my opinion is pretty much the same as above...Toyota probably takes the HP/Torque numbers + GVWR, factors in if they think the rest of the driveline is likely to grenade and cause them warranty issues and throws a number out there.
I'll leave it to others to argue if either choice is viable for towing 6000lbs regularly especially if we're talking at altitude in CO...but for lighter weights I do have a somewhat applicable comparison. My previous vehicle was a 2001 4.7 2WD Durango. Weighed in at 4500 lbs, quite similar to the 4th Gen 4Runner. While not a rocket, it would definitely run off and leave the 100 in a race. But as for towing, I would much, much rather tow with the 100. The extra 1000 lbs in front of the my 3500lb boat makes a ton of difference in regards to not being pushed around by the boat. So again, my opinion is in line with the above, unless you're drag racing the lighter weight tow vehicle is only the better choice on paper...