Last week I migrated one of my machine to RAID 1 and for the first time using HDD supporting Advanced Format (4KB sectors). I wonder new BIOS/UEFIs implementation support these HDDs natively so that they can be used not in 512Byte sector emulation. Particularly, exposing the HDD capability to the operating system.
Well, of course, the support is very probably via new ATA Command in the ATA command set spec. So, BIOS/UEFI code emits ATA Command to the drive to get info on Advanced Format support and so on. I'm still digging into UEFI spec whether there are specific data structure exposed for that support.
Anyway, GNU parted have support to optimize sector aligning for Advanced Format HDDs. I have a write up on that at: https://sites.google.com/site/pinczakko/slackware-14-software-raid-installation-on-hdd-with-advanced-format-4kb-sectors.