As far as cooling your motor, Theres really no difference, all things being the same. The main reason why the trans cooler is built into the radiator is so to heat the trans fluid up to the temp when things are cold, it put some heat into the trans fluid from the radiator.
Now, if you want to cool the trans. fluid, send your trans fluid to the radiator cooler first, then, go thru your aftermarket cooler. That will allow you to warm up the trans fluid fast when cold, then afterwards, the aftermarket cooler WILL keep the fluid actually cooler.
Now, for the folks that run automatic transmissions without a cooler in the radiator, you can run a aftermarket cooler with a inline thermostat, to allow the trans to get up to temp up faster.
Usually a min. of at least a 3 row is best for a strong street motor, for the big inch motors that are putting out some power, a 5 row is usually needed. Lower temp thermostat's and the new coolants usually will keep the high temps at bay.
Fan shrouds usually maximize the efficiency of belt driven fans and electric fans....
Copper radiators are best, they are strong, durable, and temp. transfer is pretty good. Alum. isn't as durable, and the strength isn't as strong since alum. is soft for the amount of thin cross-section available.
BUT, alum transfers the heat really well.....