What the documentation actually said was that FAT32 is included in the application's code. FAT32 is not an application, but a file system used in hard disks. You can format a HDD to FAT/FAT32, NTFS, ExFAT, EXT2(3,4), etc.
This actually means that you will have the possibility to work with partitions that have FAT32 file system. I can't fully test PCCloneEX because it asks for a serial number.