Like Zach said, they are plumbed that way to warm up faster when it's cold out. The transmission shift program is usually different until the coolant is up to 160 degrees or something like that.
I had a larger (single) transmission cooler on the Sport Trac and it was a solid 20 degree drop in the transmission, still plumbed through the radiator first. The engine coolant temp doesn't vary much so I wasn't that worried about it getting too warm. I think the warmest I ever saw it was just over 200 degrees for a couple minutes, pulling the trailer up higher mountains in Utah and Wyoming. Otherwise it hovered right around 160.
2006 F150 FX4 Super Crew - Bilstien 5100s leveled 2", 35" KM2s, 4.56 gears, Detroit locker, Eaton E-Locker, Traction Bars, AEM intake, Xcal 2
2010 VW Golf TDI 6MT