Others may be able to add additional info and/or corrections, but here is my understanding.
When you get ready to fly and connect the battery, you want the Phantom to be on a level surface, away from magnetic (ferrous) materials.
The first set of multiple green flashing lights is acknowledgement of the NAZA knowing which way the nose is pointed. I suspect that it makes a determination what level flight is based on the attitude of the Phantom; thus the need o start from a level surface.
If IOC is enabled, and Home Lock is selected, and the craft meets the distance requirement from launch point ...... If those criteria are met, no matter what direction the nose is pointed, pulling back on the right stick (mode 2) will return it to the launch point.
I believe the auto launch "feature" was addressed by a firmware update, but it still can launch itself if you switch the right switch to failsafe, after arming the motors and before advancing the throttle. Quickly switching up to ATTI or GPS will return control. This is still an area I feel should be addressed in firmware, as the Flight Controller (NAZA) apparenty can't determine what flight is, to prevent autonomous launch. Clipping on a neck strap, picking up the controller from the front, or any other action that could accidentally toggle the switch could trigger a nasty injury; especially if you didn't know how to force it to exit from the routine.
There also may still exist the possibility of out of calibration on the throttle trim may cause the NAZA to think the throttle is above a hover and activate receiver advance protection failsafe if there is no stick movement for the time period that triggers the routine.
Turning on the transmitter first is still a good habit to get into. Also, removing the props prior to connecting to the NAZA Assistant shoud be a priority.
