Had a call with the good people at Carbotech and figured it out. Seems like what we have here is a failure to communicate. Basically, the terminology being used is inaccurate.
The "pre-bedding" of pads basically refer to de-gassing the brake pads - i.e. getting the brake pad material hot so that the gasses from the chemicals, epoxies, resins, whatever get released. This does not need to be performed with the specific rotors that you plan to use on the car.
The pads also need to be "bedded" to the rotors - i.e. get a transfer layer on the rotors from the pads. If the pads are de-gassed, this can be done in a manner similar to other pads in 1-2 laps.