But sometimes you do. It's difficult to give you a list of the times this is necessary but, for example, some guitars (some PRS and Ibanez models spring to mind) implement switching options that offer various coil-tap options and this can help keep mix positions hum-cancelling. To accommodate these options, sometimes one of the pickups has its magnetic polarity 'flipped'. If you're dropping in some new pickups to these guitars, it can sometimes be necessary to consider magnetic polarity to prevent things sounding weird or unpleasant.
Then, we flip the magnet ourselves. Here's how to do it if you need to*.
Unwinding the wrapping around the coils reveals the hook-up wires. If you touch these, the world will end in a massive fireball of guitary doom. Don't poke them. Leave them alone.
On the bottom of the pickup, the baseplate will have some screws holding the bobbins to it. Loosen these but just a little—you don't want to bobbins to fall off.
Now, carefully, give the bar magnet a shove (away from the hook-up wires if they're in the way). It will emerge like the photo on the right. When it's out, don't look away—flip it before you loose track (it can be a good idea to mark it with a fine permanent marker so you don't go astray if you like).
When flipping, remember it's NOT end to end. It flips in the 'short' direction. See the arrow in the photo? Flip it that way, 180º (one half rotation).
Reassemble and proceed with your wiring, content in the knowledge that your pickup's magnetic polarity has been flipped. What was the north coil is now south and vice versa.
Now start growing your beard.
*A word of caution here. If you decide to try this yourself, be massively careful. Pickup coil wire is incredibly thin and delicate and will break if you look at it for too long. It's that delicate. Also, if the whole pickup falls apart into many different pieces, it won't be fun to put back together. This is an At Your Own Risk sort of job.