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As far as reliability I am basing this on movies like Up, The Proposal, and Transformers 2 where MTR had at least some difficulty ripping these titles and RipIt worked.
I was just posting a quick reply to try and help somebody looking for info, not be a d*ck. Luckily you have that part covered, thanks.

Apologies. I did sound like a d*ck. You've done your homework and backed up your points. Good job.
 
Did you rebuild the presets that come on the slide out menu? There is a button to select just that on the slide out menu at the bottom. The handbrake website says rebuilding the presets need to be done each time you download a new version of handbrake. Not to say that will fix your problem.

...but it did. I rebuilt the presets and then ripped a TV show using the Apple TV preset. I worked like a charm. I left the large file size box checked, and was still able to tag the show with MetaX (having enabled large file size support here), and was even able to follow these excellent instructions to create two versions for the show (for Apple TV and iPhone) under the same iTunes entry.

The show now plays everywhere: iMac, Apple TV and iPhone. Sweet.

ETA: I'm getting a slightly faster frame rate too. 30fps (for the Apple TV rip) compared to 25fps before rebuilding the presets.
 
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