I don't deal with automatics much, but at the oil change shop I worked at in high school (20 ish years ago), we had two transmission services available.
1. a flush machine that connected in place of the cooler and replaced all of the fluid (but not the filter or any nasty stuff that might have settled in the pan)
2. remove the pan, change the filter, and refill. Because so much fluid is held up in the transmission/torque converter, this only resulted in about a third of the fluid actually being replaced, and was the only one that ever resulted in a drop of hot, filthy, burned ATF dripping past my safety glasses onto my eyeball.
Either option always seemed like a compromise to me, so I'm interested in what is the right way.