There is a big difference. They make fluid flush machines and fluid exchange machines.
Flush machines use there own pump to force new fluid into a transmission and push the old fluid out. That is the best way to have clutch material get moved around and clog things like the valve body or feed lines inside the transmission.
Exchange machines and or doing the method in the previous posts use the transmission pump itself to do everthing. There nothing forcing fluid in and out and way less chance at internal issues. There are many vehicles out there with no internal filter or that have no way to remove the pan because they don't have one. They use plugs on the side to determine fluid level, so exchange machines work great, have it do the work for you then top off the fluid untill it comes out the full level plug hole.
