I also have the rather confusing Ford manuals. I've finally surmised that the process outlined is an effort to fairly thoroughly purge the tranny and the cooler ... going thru about 13 qts of fresh fluid in the process. But you can't push out the old with the new and not have "fluid mixing" in the process. And unless you drop the pan, you can not wipe out the pan and clean the magnets.
So, like many others, I think dropping the pan and replacing the 6 1/3 qts that drains ... but doing it twice as frequently as someone might with the Ford process ... is the better practice. As long as the fluid is fairly clean, there is no reason to suspect the cooler needs "flushing".
I believe this is the practice suggested by the Haynes manual.
By the way, the pan gasket is reusable.