Many shade tree mechanics will change only a quart or two of the ATF if the transmission fluid is long overdue for changing. Then, a month or two later, they'll change another two quarts. The idea is that a full fluid swap will "shock" the transmission and cause it to fail, something that has many anecdotal examples on auto message boards. Does it work? Who knows.
As sort of a counter to that, one of the common "shade tree" methods is to drop the pan, which typically only gets about half the fluid out anyway rather than draining the whole transmission.
Most shops now use the "flush" method where they connect the transmission cooler lines to a machine that flushes out the old fluid with fresh while also cycling through the different gears. If this is done right, I think that it uses about 1.5x the total transmission volume, but does actually change all the fluid.
There may be some validity to it "disturbing" things in the transmission, I think that's likely still due to a transmission that's long overdue for service and is on the way out. Being proactive with fluid changes(as I said, I try to do it every 30K miles, which is what the guy who designed the transmission in my car told me to do, although I'm not as on top of it as I should be) can prevent a lot of this.