I have two hard drives, one formatted with NTFS and the other with exFAT. Both have an allocation unit size of 16384K. However, when I copy files between the two disks, the same file will take up significantly more "size on disk" on the exFAT drive compared to the NTFS drive. Why?
Are you sure your allocation unit is 16 MB??? Anyway, this is because NTFS can store small files within MFT (Master File Table) as internal attribute, unlike exFAT, where even 100 byte file occupy one cluster.