Even though HDDs are addressable by LBA since decades, Microsoft still uses CHS for stupid stuff in the MBR even in the newest versions of Windows. That's why changing CHS translation in any way leads to a non-booting Windows. Or why sometimes partitioning gets completely garbled if you partition with Linux, then change a partition with Windows.
So when Windows creates partitions, it still tries to align to track boundaries. Especially at the end of the disk. Which is not only Microsoft's fault because there are some ancient BIOSes that would restrict access to incomplete CHS tracks at the end or even have an off-by-one in the track counter. Still, those should have died off long ago, and it usually works fine if you partition with Linux and do not touch the partitioning in Windows.
tl;dr: Legacy reasons.