we have both.
the athc is a head that mounts to the gantry that has a z-axis on it. it has a sensor for determining the force on that axis so it can touch off the work piece (zero itself before each cut) and move up to the set torch height. it also has a box that controls it and acts as the interface.
the 3rd axis is a heavier-duty third axis with more travel.
it doesn't seem like they could have integrated the two without either 1) making the unit really expensive, or 2) making some performance sacrifices.