Just so I get this clear, at what point should I see the quick green blinking lights that show the home point has been set, before compass calibration or after? If it's before calibration is the home point set as soon as the phantom is powered up?

There are two sets of fast flashing green lights after power up independent of the compass calibration, the first one approx.  30 seconds after power up that confirms that orientation has been saved,  the second set whenever 6 or more Sats are locked onto. However note that the homepoint will only be saved if you start the motors the first time after the 2nd set of flashing green lights or right at the 2nd set of flashing green lights if your motors are already running ( can also be in the air ).

Yes, there are two sets of flashing green lights. First one: 30 seconds after you power on the autopilot system, this one is the Course Lock. Second one: Before takeoff, the current position of the aircraft will be saved as home point when you start the motors for the first time after 6 or more GPS satelllites have been found for 10 seconds, this one is Home Lock.
Please also go to the User Manual of NAZA M V2 for details. Page 19.
http://download.dji-innovations. ... _Guide_v1.26_en.pdf

Sophie,  as a side note the Naza-M V2 IOC Wiki entry has the "Automatically" and "Manually" label reversed in the table (V1.26 PDF Manual shows it correctly)

Ok, thanks guys.