A custom tune will be out of range for the STD narrow band O2 sensor, which only when 14.5:1 AFR is active in the fuel map such as when idling and in the lower RPM Cruise mode(s). The STD O2 sensor only tells the ECU if the AFR has not reached the point of 14.6:1 AFR like a switch to confirm correct mixture. A custom Tune and mapping will not work with a std O2 sensor as the AFR is generally way out of range for a narrow band O2 sensor to functon, Custom / Dyno tuners use a wideband O2 sensor to actually measure and confirm real time AFR and adjust the fuel mapping and ignition timing in some cases to meet the requirements of both the rider and the engine configuration, this wideband O2 sensor is removed after the tune is completed. Some Auto-tune systems are available with their own O2 sensor such as the PCV but they also require replacement of the STD O2 sensor and it still must be disabled through the ECU. That is the reason why O2 sensors are disabled in Tune Ecu with a custom tune.
BTW - some custom tunes still utilize the O2 sensor function and leave the O2 sensor switched on, if that tune has been developed that way then simply follow the tuners advice (as long as you can trust it).
I hope I haven't confused you totally, If I have then - sorry for that.
John