They're just there so that you can aesthetically centre the dot in your magnifier view. Shouldn't affect zero, as this is made on your XPS itself.
I have had a few times (when using my G33) where I've felt that my rounds have been slightly off left of aim compared to just using the XPS alone, but this is probably down to the magnifier just magnifying the bit of parallax you get at shorter distances (25m).
yep just to ensure that the magnifier is centered with the optic, it looks a little weird when it is 'off' so just mess with it until dot is centered and leave it alone. should be GTG.