While I can certainly see advantages to having the arrow under the dominant eye, and try to do it myself, many good shooters don't do that, either because they shoot with their non-dominant eye over the arrow, or because they consistently shoot with their eye a little to the side of the arrow. If I had to make a choice between naturally drawing to an anchor where the arrow was consistently in the same position, although not directly under my eye, and having to think about drawing to a contrived position that wasn't natural to me in order to get my eye over the arrow, I would choose the former.
As far as how one would get used to that, an instinctive shooter just gets used to pointing the bow where it needs to be pointed over many shots without consciously lining up anything. A reference shooter just gets used to holding the point of the arrow a little to the right or left, and eventually doesn't even notice that he's doing it.
Also important is to draw the arrow to your head without tilting or moving your head, although some good shooters do tilt their heads. Also important is to be able to shoot the bow at any reasonable cant, although most people do have a natural cant (or no cant at all) where they shoot best.