I have always heard that flushing a transmission can cause the loosening of particles which might find their way into some of the modules or internals. I have always dropped the pan and cleaned the metal filings off the pan magnet, replaced the filter then pan gasket, and filled her up with new fluid. I've never worried about some of the ATF left in the converter. This saves on the amount of ATF used and if you change often enough then it isn't a problem.
My 2500hd with Allison transmission gets a spin-off filter every 10,000 miles and a fluid change every 30,000-35,000 miles. The Allison has an internal filter as well but when I change it for the first time, I will add a deeper aluminum pan and extended filter.
'01 2500hd ext. cab, 8.1 litre gas, 5 sp. Allison auto
3.73 rear end
Mag-Hytec rear diff cover
Amsoil Dual by-pass oil filtration system
Amsoil synthetics all around
265 watt AM Solar, Inc. system