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What type of backups are you looking to do? Are you just going to mirror your local drives to a share on the remote system? Or are you going to use something like Windows's built-in backup manager to concatenate your files?
In either event, the filesystem on the server's drive will have no consequence to the Windows machine. The Windows machine just knows the server supports the SMB/CIFS protocol, and sends it's data along; it has no idea what happens to the data after that point, and doesn't particularly care.
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