Change cluster size - only used space?

I tried to read this KB article http://kb.acronis.com/content/14636 and I didn't understand it. How can cluster size be different for the used space and free space on the same partition?

If

NTFS refers to physical locations on a disk by means of logical cluster numbers (LCNs). LCNs are simply the numbering of all clusters from the beginning of the volume to the end. To convert an LCN to a physical disk address, NTFS multiplies the LCN by the cluster factor to get the physical byte offset on the volume, as the disk driver interface requires.

is true, how can it deal with two different cluster sizes?