In-camera settings have no impact on the RAW/NEF files the camera generates. They're really conversion settings used when the camera creates JPEGs from the RAW/NEF data. If you choose to store your photos in JPEG format, these settings are critical 'cause you're stuck with their results. If you choose to store in RAW/NEF, they don't matter at all except as conveniences which can save you some steps in Nikon Capture. For best color results my experience strongly suggests shooting in RAW/NEF.
Here are some of the sites which helped me figure this out:
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