Depends On Wheel Size, I Think
I don't believe the info in the '03 chart is correct. My '03 Limited V8 w/17" wheels has the larger front rotors - I measured them.
While this is my only data point in this discussion, I believe it's very likely that all the 4th gen 'Runners with 17" wheels get the bigger front brakes, regardless of model.
This is consistent with good engineering practice and Toyota's policy for the 3rd gen cars, in which cars with 16" wheels got bigger rotors than 15" wheel equipped cars.
Best regards.