This is a serious issue for 4K-sector hard drives only, such as those produced by Western Digital using "advanced format" drives. For most other hard drives using a 512B sector size, there is no problem. Windows7 has a 512B emulation mode for "misaligned" and legacy drives. Linux and MacOS have no issues since this is a NTFS problem.

The problem is that, for 4K-sector hard drives, buffer reads and writes are in 4K blocks, not 512B blocks. If there is a misalignment in sectors to blocks, then the overlap forces two block reads for every sector read. This results in potentially doubling the duty time of the hard drive unit.

However, for legacy drives, reads of 512B sectors in 512B block sizes are always aligned.

One exception is Solid-State (SSD) units that can be helped through alignment in that they are advanced-format as well. Paragon Software provides an alignment tool (Paragon Alignment Tool [PAT]) that can be purchased online. Western Digital provides PAT free of charge, branded for their hard drives.

Joel