I believe the accuracy you want depends on the coupling faces of the magnet. If you have 3 or more 'spots' that match up of equal size and mirrored placement, I'm quite sure the alignment would continuously be sub millimeter, but this assumes there's no external force on the magnets since an inward force could create substantial friction to keep the alignment from being perfect. Likewise with a lateral force.

If you want it to be less accurate and leave some room for error then I'm sure you can offset each mirrored 'spot' off slightly in different directions so they're all equally lop sided with respect to each other.

Presumably it could scale all the way down to the domains on a hard-disk platter, but there are probably intermediate ranges of magnetic domain size where no practical techniques are available.