Check your ~/Library/Preferences/ByHost
the com.apple.systemuiserver.MACADDRESS.plist will contain a dontAutoLoad key for time machine as soon as you turn it off. So far all of my testing leads me to believe that this is the only location to prevent the TimeMachine menubar item, and requires the mac address, which obviously makes it tough for deployment or user templates unless login scripts change the MAC on login.
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