My personal experience as well as that of every other owner of a Tranasxle-cooler-equipped car, is that the warm-up times of the trans fluid is NOT adversely effected by the presence of the cooler. In other words, virtually every owner of a GT has experienced some 1-2 shift notchiness when the car is cold. Most remedy the situation by double-clutching or by skipping 2nd gear entirely during the warm-up period. This warm-up period is, in my experience, limited to the first 2-3 miles of driving. Perhaps it is longer in colder conditions. (I'm in SoCal so what do I know about cold?) Anyway, the point is that with the installation of a Transaxle Cooler, be it the Cool Tech, Ford Racing, or home-grown variety, experience says that the warm-up times are NOT elongated. So, even with a transaxle-cooler-equipped car, you quickly reach a functioning operating temperature (as evidenced by the silky-smooth shifting) but you have protection against adversely high temperatures that can be detrimental. Ford could have easily limited their recommendation to just race-track driven cars but chose to say, "A must for aggressive driving and open track events."
In my view GT owners should, at least occasionally (and under safe conditions), "drive aggressively", otherwise why own the car? The aforementioned cooler alternatives all use factory-provided mounting locations, leverage the -AN fittings already on the car, and provide peace of mind of having a component that was so clearly designed to be on each car when it left the factory. Perhaps we'll never know the real reason but clearly several owners here can attest to the delayed availability of the Ford Racing Coolers early-on which I believe may have contributed to the "let's push it to the aftermarket" decision so as not to delay the availability of the car itself.