They fed you a line that should scare anyone, it would be the equivalent of trying to back flush your engine. You would have to fill the crankcase full before anything would come out the valve cover. The same would apply to an automatic trans, the thing is not full to the brim with fluid and since they can't really force it through the engine has to be running and they can't pump it against the transmission pump...
Unless they were backflushing the coolers...
I change the filter myself and have mine flushed (no converter plug) I just did it a couple months ago and the truck has 104k miles on it and still shifts great. It had just been done when I got it at 25k and I did it at 60k too.