The point of that tool is to relearn the positions. The older models could be done by entering a programming mode using the DIC, the newer ones require a tool.
The car receives four signals, one from each wheel, of the amount of air pressure in each tire. The car doesn't know WHERE those four tires are. It's up to you to program what tire is where. You go to each wheel, starting with the left front and let air out the tire (older version) or place the tool next to the valve stem (newer version). This tells the car that the tire losing pressure or the one that the tool is near is the left front wheel. You repeat the process in a clockwise rotation with the right front, then right rear and end with the left rear. You could go in whatever order you wanted to, and the car would still program each one in it's clockwise order because it doesn't know you went to different corners outside of the clockwise pattern. All this would do is report the pressures incorrectly so if you had a low tire, it may report it as being on a different tire. When you rotate the tires, you have to tell the car that "X" sensor is now in the left front position, "X" sensor in now in the right front position, etc.