The FAT32 is a file system on which a max file size of 4 Gigabyte can be stored.
exFAT is a new file system on which a max file size of 16 Exabyte can be stored. Currently this file system is used only for Flash drives and not for HDDs.
The above file systems have no built in file permissions ( except for the basic file attributes like, system, hidden, read only and archive).
NTFS is a robust file system with built in file permissions to make the files either accessible or inaccessible to other users. This is an industry standard file system from Microsoft and is widely used by windows OSs like Win NT, Win 2000, Win XP, Win Vista and Win 7. This file system can store a single file of max 16 Exabyte.
The link below explains the differences between exFAT, FAT32 and NTFS. exFAT Versus FAT32 Versus NTFS
and NTFS vs FAT
When a file from NTFS file system is copied to either FAT32 or exFAT, the full contents of the file are copied, except the streams data and the NTFS permissions.
So for the application which has created the file it does not make any difference, whether the file is read from NTFS partition or FAT/exFAT partition.