Is it really that important at the moment if your playing flat on the lowers, it sounds like and I mean no offence that your still relatively new as a player, with muscle development in the lips those lower notes will eventually come up to pitch with no issues.
This may have been why your teacher was not worried about it, because with time it will correct itself.
Its like if you remember the first time you may have played a scale and you go all light headed and whoozy (it was that way for me when I started flute), over time that feeling dis-appears, our body learns adjusts and overcomes.
As far as your head cork, just insert your flute rod into the head joint and the line should be pretty close to a visual centre of the embochure hole, if it is, don't play with it, just leave it, fine tuning the head cork IMO is just for tweaking the third octave and your only dealing with about .1mm in either direction. This is also subjective to the player, whats good for one person is not definitively going to be good for another.