I certainly would not call myself an expert on the 2LTE as found in the Prado and Surf. BUT I have worked on a fair number of them now and can say, without a doubt, that there are multiple causes to the early demise of the 2LTE engine.
The radiator capacity is more than adequate when working with reasonable efficiency. However, many, if not most, JDMs arriving from Japan have horribly under-serviced cooling systems. Almost every cooling system I have seen has contained an inadequate amount of coolant for corrosion protection and is severely plugged up as a result (corrosion and water mineral products precipitating out of soluton).
I believe that many 2LTEs suffer from over-fueling issues, some of which is related to driver error, but much of it is a lack of service and/or improperly performing injection pumps. Over-fueling leads to excess heat that tends to localize in the head and exhaust system.
The heads I use, and have used in the past are all genuine Toyota 3L heads.
Here's an example of a 2LTE head and block that had a the typical coolant to cylinder leaking problem. Others we see have pressurization of the cooling system, which is typically a one way movement (no coolant enters the engine).
~John