Technically, every lossy encoding loses information (read: quality). If the bitrate is high enough a human won't be able to tell the difference, though. We call that "transparent". So the MVC should in theory be better but it might not make any difference in practice if you use sufficient bitrate (i.e. sufficiently low --crf or sufficiently high --bitrate).
P.S.: While it is possible to employ lossless encoding (in x264 using --qp 0) the resulting file would be much larger than the original BluRay.
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