Some rotating hard disks are said to be quicker if reads/writes are aligned to big blocks (4096 bytes aligned read/write), and unfortunately the usual PC partition table make the usual first partition start at sector 63 (sector size 512 bytes) - completely unaligned.
Some bootloader use those sectors at the beginning of the disk (but not all bootloaders use them).
If the filesystem code could detect unaligned start of partition, it could insert a padding sector at beginning...