I suggest you to pick up AnyDVD HD and use AnotherEAC3toGUI under VMWare/Parallels:
http://www.curtpalme.com/forum/viewtopic.php?t=17002
That will create you a 1:1 MKV copy of the original movie, including lossless Dolby TrueHD/DTS-HD decoded as FLAC (something that MakeMKV still doesn't do).
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Interesting assertion. MakeMKV repackages the Bluray structure and doesn't change anything. The audio tracks are all there. If your point was the decoding audio tracks as FLAC part, if that is somehow desireable (I don't understand why one needs to decode audio tracks as FLAC) when backing up Blurays, oh well.
I also don't know why you would run Any DVD HD in VMWare/Parallels, but to each his own. Video encoding is processor intensive, and you'd use less resources running Windows 7 (or prior) natively under bootcamp rather than emulating using VMWare/Parallels in OS X.
When I make backups of my blurays, the only thing I have to do in Windows (if I want to burn a copy of just the main title/with English subtitles to BD-R) is use ImgBurn to burn it. And that's because ImgBurn is open source freeware--I don't know of anything that can burn a bluray under OS X that's readable by a set top bluray player, other than Toast. If one wants to pay for software, the combination of MakeMKV and Toast would let you copy and burn under OS X.
I don't begrudge software developers from making money, but the price of AnyDVD is a lot of money to spend for what it does vs. open source alternatives.
Plus which, when I tried the evaluation copy of AnyDVD HD two weeks ago, it could not rip the one bluray I threw at it (I cannot recall if it was Inception, Due Date or Unstoppable), and said I had to pay for AnyDVD HD to get the latest updates--sort of defeats the purpose of a free trial.