perhaps I'm using the term flush improperly, maybe the dealer shop is only doing an exchange?
I've read in a few different places that some guys unhook a line to the transmission cooler and pump all the fluid out by running the engine until ATF stops flowing, what do you guys think of that method?
Check and make sure thats what they are doing. Most of them have those machines now and a dealer should realize thats the only way to do it with any efficacy.
These machines do essentially the same thing as unhooking the return cooler line and routing it into a container. They tap into the line to route the old fluid into a container that has a bladder seperating the old fluid form the new. As the old fluid fills the container it forces the new fluid into the trans.
You can do the same thing by yourself in the drive way by just removing the rear cooler line and routing it into a bucket to catch the old fluid. It takes at least 3 times refilling and about 20 quarts to fully flush all the old fluid out that way but it works.