Ignoring the FAT32 vs NTFS question, more important is the fact that you have your backup partition on the same physical drive as your "C" partition or drive. This is not a wise thing to do. If the drive mechanically fails (which they do - all too often) then you will have lost your operating system and its backup.
Far better to move the backup partition elsewhere. Why not on the external drive and also use Acronis Secure Zone so that you cannot accidentally delete or otherwise alter the backup unintentionally.
Regarding the FAT32/NTFS question, I think Acronis was developed in teh days of FAT32 and they don't see any reason to change the way their good software operates - potentially introducing problems if they did.