Okay, so as I thought, doesn't make a huge amount of sense. Thanks for clarifying.
The main power source has XT60 connectors, and as I mentioned in another post, I am going to change that to Deans. Meantime though, I am powering the Pixhawk from servo rail output pins, and USB during the calibration process (using APM 2.0). The calibration process isn't working (another post)
Is there a problem with not powering using the main power port?