The Scantool pulses the gate to engage the ABS to allow the fluid to be flushed. If you stick to the basic style of flushing, the ABS module gate stays shut and you'll flush everything out.
I've always done the poor mans way, that is, use a One-man bleeder with a reseviour. You pump the brakes enough times until the fluid that comes out is clean. I go around the vehicle twice. I start at the driver rear and go all the way around and do the driver front last.
When you use this method, your using the brake pedal and booster to push the old fluid out(Keep the reseviour topped off!!!) Since you can push the pedal all the way to the floor, this puts the brake pedal past it's point of normalcy. Since brake fluid is veryy corrosive once exposed to the elements, minor leaks past the booster seals are common. This can cause rusting on the piston sleeve. The piston sleeve runs in/out of a seal. Since the brake pedal only goes down 2-3" in everyday driving, rust may have set in on the piston shaft in the "unused" area. When you flush, your putting the pedal so the possible rust areas are scuffing along the internal seal.
Because of this, I really reccomend putting either a block under the pedal to limit the travel to no more than 70%. If you put the pedal to the floor the first time you'll get an idea. No one or a couple of times isn't going to hurt, but you pump your brake pedal a hundred times in this whole process.