File splitting simply separates files into chunks that can be rejoined at a later time, the rejoined file will have the same MD5 hash.
If the only two platforms you're using are FreeBSD and Linux, why would you pick NTFS or FAT for such a thing? it's quite inappropriate.
FreeBSD has support for ext2, and ext2 is supported by Linux natively.
There are tools for creating ext2 filesystems on *BSD, but you should probably do this on Linux... once created it can be mounted normally.
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