It can be a lot clearer organizationally to keep things created intentionally on a separate partition, to distinguish from all the stuff dumped into your profile by applications. And if you fill up the "data" partition accidentally it doesn't prevent the system from functioning.
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%APPDATA% lives in %USERPROFILE% as far as I can tell.
Since you already back up your %USERPROFILE%, which supposedly lives on C:, what benefit is there in having "data" on a separate partition?
It can be a lot clearer organizationally to keep things created intentionally on a separate partition, to distinguish from all the stuff dumped into your profile by applications. And if you fill up the "data" partition accidentally it doesn't prevent the system from functioning.