It is a bit hard to explain in words how this process is done if you haven?t seen a lathe machinist work. Anyhow I'll try to explain.
The Rotor is secured to the car at its hub. The hub is supported via the wheel bearing upon which it turns. The rotor, when it was manufactured at the factory was produced in (most probably) one shot on a CNC machine. The CNC machine has the advantage the multiple operations can be done WITHOUT REMOVING THE DISC FROM THE MACHINE. And because all the operations on the rotor were done without removing it from the machine, all dimensions and surfaces are correct with respect TO EACH OTHER. Also it has to be kept in mind that in order to ensure that two components (hub and rotor) sit against each other CONCENTRICALY usually a step or seat or collar or tapered seat screws are provided.
With that back ground, we now come to the normal lathe machine which are used in the market to tool rotors. Lathe machines typically have a three jaw or four jaw chucks. Chuck is the part of a lathe machine that holds the rotor and spins it to allow tooling. If the chuck could hold the rotor in the EXACT same way in the EXACT same place as it was fitted to the car, there would be no need to zero the rotor. However, that is not the case, the rotor is held on the chuck most probably from it outer diameter. Since the rotor is held from a different place as compared to its fitting on the car, it's centre on the lath is not is not in the same place as compared to if it was on the hub, a process has to be done to MAKE the centre EXACTLY same as if it was fitted to the hub. This process is called "zeroing" or "centreing". While centering the rotor both axial and concentric "zeroing" has to be confirmed. There are a few methods to do this, (1) fabricate a fixture or jig specifically designed for the rotor that fits in the lathe chuck; this fixture once certerized in the chuck automatically holds the rotor concentrically. (2) Use specially designed tapered cones to hold the rotor during the tooling process. Taper cones also automatically hold the rotor concentrically. (3) Use a double dial method to certerize the rotor axially and concentrically. Of course let us not forget that there a lathes specifically designed for the singular purpose of tooling rotors. These machines have no other purpose what so ever. Such machines are not found easily in the workshops.
With all these "not so easy" and correct methods of "zeroing" the local ustaads to a short method of spinning a rotor, touching the tool lightly to the rotor to scribe a line on it. Since the rotor is wobbling on the lath, some part is closer to the tool and some part is far. The ustaad keeps moving the rotor about in the chuck until he gets an even line on the rotor. The accuracy of this zeroing method is dependant on the skill of the ustaat. There are more chances of ruining the rotor that has been "zeroed" by this method for tooling than getting it right. Thus it is not advisable to tool rotors plus it is unnecessary to do this on every pad change.