- Does LBA always specify sectors as 512bytes 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 won't boot from such disk at all.
- Also is the reason the logicle 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 first partition on LBA sector 2048 (1M alignment). It may have any CHS coordinates, they does not matter anymore.
In Windows XP and previous versions, 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 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/Windows7.
- 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 partition was created in pre-Vista FDISK and is misaligned itself.