Eu perguntei na lista de discussão util-linux (o programa '' fdisk '' pertence ao pacote util-linux). Você pode ler o tópico inteiro aqui . Deixe-me citar as partes relevantes.
Kay Sievers disse:
It's a de-facto standard, which Windows does too. The first megabyte is reserved here for a boot loader or any other management data that could be needed for a disk or box to boot from.
Karel Zak disse:
The real reason is that 1MiB is ideal offset to keep partitions aligned on almost all random hardware. This offset is compatible with 512-byte, 4096-byte sector devices, many raid devices as well as old broken WD disks where physical sector size has been incorrectly reported. You can use dd(1) to move your PT + data to another device without care about physical device topology (I/O limits), etc.
It's also important to keep your partition sizes aligned to MiB -- this is for example default in fdisk if you specify the size in +{M,G} convention.