Trying not to beat a dead horse here but I have spent a day or two researching this topic and since this is one of the only 4th gen threads I have found I will share my findings.
The topic of warming transmission fluid through the radiator was well explained by a Ford transmission engineer:
Posted By: Mark Kovalsky on 09/02/10 08:44pm
The in tank cooler will NOT warm the trans fluid in cold weather. In cold weather the coolant in the tank where the trans cooler is located will be near ambient. If it's 0°F out the coolant in this part of the radiator will be about 10°F or cooler!. This is from actual testing I did as a transmission cooling engineer. After extensive testing on many different vehicles in temperatures as cold as -40°F I never found a condition where the in tank cooler warmed the trans fluid at all.
Putting the radiator cooler after the air to oil cooler will result in warmer transmission temperatures when you need to cool the trans. The system is more efficient going from the trans to the in tank cooler to the air to oil cooler and back to the trans. That's the way all the manufacturers route the fluid because they have people that can calculate this is the right way to do it, and an extensive test program to prove it, too.
Mark
Former Ford Automatic Transmission Engineer, 1988-2007
This post and his work experience in transmission cooling to back his statement can be found in the links below.
RV.Net Open Roads Forum: Towing: Bypass factory trans cooler or keep it?
RV.Net Open Roads Forum: Tow Vehicles: Bypass radiator/tranny cooler combo?
That being said, he and others agree that bypassing the radiator transmission cooler is not recommended because it lowers the transmission temperatures more effectively than external transmission coolers. Can you put big enough external coolers to safely bypass the radiator? It all depends on a lot of factors that are unique to every driver, vehicle, and environment. I am not going to go through all the different scenarios I have read, but there are people who haven't had any problems bypassing and people who switched back to radiator+external cooling setup to reduce high transmission temps they encountered after bypassing the radiator.
As for me, I will be replacing what I believe to be the oem radiator (without bypassing) and setup/monitor a good trans temp gauge. Later down the road I might upgrade my factory external transmission cooler and bypass the radiator to see the difference in temps. I have also pondered the idea of adding a valve to a bypassed system to allow the use of the radiator cooler when needed. If anyone has any thoughts or experience with that please share.