Pole pieces have nothing to do with "out-of-phase" issues. If you're getting the hollow, weak, nasal funky tone associated with reverse phasing, it's either a magnet or wiring problem.
There really isn't a "too low" or "too high", except to say that if the pole pieces are buried below the surface of the bobbin, it's probably too low for any sort of 'normal' sound (though some might prefer that). And if the head of the pole piece is completely above the the surface of the bobbin to the point where you can easily see the threads of the pole, it's too high, though again, though some might actually prefer that too.
As for the effect of raising vs. lowering: Raising the polepieces will increase the overall output but will also give it a brighter sound -- lowering will do vice
versa.
It's all ultimately a matter of taste but somewhere between the two extremes described earlier is where you find your conventional/classic guitar tones. I adjust according to the basic tone of the guitar -- if it's warm and dark, I set the poles kind of high for a little more brightness, and lower them closer to the surface of the bobbin if the guitar needs a little more beef. I also adjust on a string-by-string basis -- some strings may sound a little weak compared to the others and need a little help from a higher pole piece.