How will it affect the sound if the strings don't go over the center of the corresponding magnets, and are slightly off (say, the E strings would each be off by 1 mm) ?
It might be a little quieter but probably not that much different if they're all off a little bit
You would get reduced volume and possibly lose some dynamics(in terms of what the pickups pick up). Thats about it.
you can raise the pole (if adjustable) or raise the E side, to compensate.
on my MIA strats neck pickup the e is hardly over the magnet at all but the sound seems unaffected
I see. Thank you.