Proper alignment of partitions on an Advanced Format HDD using Parted

Parted is just being overly conservative. The usual practice these days is to align partitions on 1MiB (2048-sector) boundaries because this works on Advanced Format disks, on certain type of RAID setups that require alignment, and on most SSDs. For an Advanced Format disk, so long as the alignment is on a multiple of 8, you're fine, and 2048 is a multiple of 8. The lost disk space is puny -- 0.0000336% of your total disk space, if I did the math right and didn't mistype anything. So don't worry about it; just use the 1MiB alignment.