You just need to shift the headstock end of the neck "up" a bit to align those E strings better.

Also, perfect pole/string alignment is 99% a visual thing. The magnetic field of the pole pieces extends well beyond the edge of the poles themselves. A mm one way or the other will have little to no effect on tone or signal output.

An interesting little experiment with this is to plug an unstrung guitar into an amp, tap a tuning fork, and hover it over and around the pole pieces. (use the area between the two vibrating "tines" where the vibrational energy is the strongest)
You can sort of "see" the magnetic fields are.