If your motor has hall sensors, you could use sine initialization mode 0. The motor will drive the first revolution based on the hall sensors, just when it is started.
Adidtionally, perhaps you could do the first motor revolution with a high acceleration and high velocity? This way, the coarse behavior of position regulator in combination with the hall sensor commutation will not really show up and will be ended quickly.
An other idea using initialization mode 3 with encoder N channel: When you switch off the device, you could park the motor at a position just very near to the encoder N channel. Now, run the initialization in the correct direction after power on. It will find the N position very quickly then.