The "Copy files if modification date difference is not an exact multiple of one hour" option allows files whose modification times may have been offset by a time zone or Daylight Savings Time change to be properly synchronized.
It may be useful: (1) when a synchronization or backup is done with a disk which may have been last written in a different time zone; (2) when connecting to a file server in a different time zone, and (3) when two disks are formatted differently, one with Mac OS Standard format, and one with Mac OS Extended format. In each of these situations, the files' modification times appear to be different by exactly some number of hours.
This option acts to prevent some files from being copied. If two files' modification times are different, but the difference is an exact multiple of one hour, the newer file will not be copied.