You get a huge performance impact if the OS doesn't align the clusters to the sectors. From the wikipedia article: The translation process is more complicated

You get a huge performance impact if the OS doesn't align the clusters to the sectors. From the wikipedia article: The translation process is more complicated when writing data that is either not a multiple of 4K or not aligned to a 4K boundary. In these instances, the hard drive must read the entire 4,096-byte sector containing the targeted data into internal memory, integrate the new data into the previously existing data and then rewrite the entire 4,096-byte sector onto the disk media. This operation, known as read-modify-write (RMW), can require additional revolution of the magnetic disks, resulting in a perceptible performance impact to the system user Most of the OSes correctly align the advanced format sectors.