First, ones and zeros on a harddisk platter are not magnetic north and south, they are different frequencies of an FM sine wave.
Second, the formatted tracks on a harddisk don't line up physically. The start of the track is wherever the head was when the controller was told to format that track.
Third, Sectors aren't written in precise places inside their formatting. The low-level formatting process writes headers across the track that are used later to find the data. There's enough extra space between those headers that a sector of data will fit there, based on the ability of the controller to read where the sector starts and be able to write it.
If you really need to write magnetic north & south to specific spots, you should look at Floppies. Floppy disks have a hole to mark one spot on the disk, so the start of track comes much closer to lining up. You can even write ones and zeroes instead of FM patterns if you have an old Apple II, which didn't use FM encoding.