No, it's not totally independent. Most settings are used for the 2D and 3D versions (like the selected streams, 720p, CRF value or bitrate). Of course, the 3D specific settings (like SBS, 3D subtitles...) are ignored. And some other settings are ignored as well for technical reasons, like the black at the beginning or end of the movie, because the original AVC stream is re-encoded directly and there is no avisynth script and therefore there are less possibilities. But anyway, the overall quality of the 2D version should be identical or very similar to the quality of the 3D version.
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