I am not an expert on file systems, but I can easily state that there
are advantages and disadvantages in both files systems. However, I
think that NTFS overall is best suited for larger files, plus it
supports compression and encryption should you chose to use
Microsoft's weak EFS. (Which in itself is really a bad idea) Moreover,
I see no reason to use FAT32 on any of your drives…there is no
sensible point or advantage. You have a lot more control when using
NTFS. I don't think it makes any difference as far as security goes
when formatting an encrypted container. You can use both file systems.
Still, I recommend NTFS especially if you're going to format large
containers or whole drives.
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