LBA and sector size

• Does LBA always specify sectors as 512 bytes even if the drive is formatted with 4K sectors?

Yes, a lot of code in the world was written in the times of exclusive domination of 512-byte sectors. This code cannot handle any other sector size, so BIOS / disk hardware always emulates 512-bytes sectors regardless of actual sector size. Otherwise, 95% of operating systems just wouldn't boot from such disks at all.

• Also, is the reason the logical drive geometry is different from the physical drive geometry – to maintain backwards compatibility with old standards and limitations with CHS?

There are boundaries in CHS addressing system. 1 ≤ S ≤ 63, 0 ≤ H ≤ 255 (and sometimes 0 ≤ C ≤ 1023). It is the reason why logical geometry exists and is different from the physical geometry.

• If the drive-reported geometry is not accurate, why do partitions still need to start at sector 63 (if that is no longer always the correct cylinder)?

Since Windows Vista, FDISK creates the first partition on LBA sector 2048 (1M alignment). It may have any CHS coordinates; they do not matter anymore.

In Windows XP and previous versions, the first partition was created on CHS sector (C=0, H=1, S=1) which usually maps to LBA sector 63 (if logical geometry of this disk has 63 sectors per track). Some USB flash drives have logical geometry with 32 virtual sectors per track, so the first partition starts on LBA sector 32 for them. In any case, all of this has nothing to do with actual disk geometry, performance reasons, etc – it's a pure tradition, terminated in Vista/Windows 7.

• Are clusters aligned with the start of the partition or the start of the disk?

Clusters are always aligned with the start of the partition. So they may be misaligned on disk, if the partition was created in pre-Vista FDISK and is misaligned itself.

LBA itself can apply to any sector size, but hard drive sector sizes have been 512 bytes since the start of the PC, and all hardware and software has been hard-coded with that assumption. So rather than wait for new systems and operating systems to support 4K sectors, the drive will appear externally as a 512-byte sector drive.

CHS has been dead since LBA48 was introduced in 2003. CHS is limited to 128 GB, so every drive greater than that size doesn't support CHS (take a look at a modern drive; it won't have a CHS value on the label). In the case all hardware and operating systems had already been updated (Windows 98 added support for LBA).

Even with CHS, the physical drive characteristics didn't match the CHS values. Seriously, no hard drive ever had 255 heads. The drive’s controller would internally convert the CHS values to LBA.

Partitions don't have to start at sector 63 – that's an old DOS limitation. DOS required that a partition didn't split a cylinder boundary, and CHS has 63 sectors for cylinder. Microsoft up to Windows XP had decided to maintain compatibility with DOS (it was possible to dual boot Windows 98, ME and XP on a FAT32 partition). Until 4K sectors, there wasn't a problem with it.

Finally, to answer your question: clusters are aligned with the start of the partition, not the disk. Which is why it is important that your partition is properly aligned on a sector boundary.