Gives me the same problems as Handbrake. I have a disc with 7 TV episodes on it; most have an alternate audio track commentary. When I set MTR to do a Title-Chapter Extraction (or "Title Only Extraction, exact same results), and then click on the up/down arrows to select which episode I want, I have EIGHTEEN segments to choose from - why 18 when there are only 7 eps on the disc?? If I extract all 18 segments, I will end up with multiple copies of each episode, and those copies are IDENTICAL - no way to select I want the audio commentary, no way to figure out which segements are duplicates - I've wasted HOURS ripping these discs, only to end up with 2 or 3 copies of EACH EPISODE, all with the identical soundtrack, and no way to choose the alternate commentary.
If you definitely want to store each episode as a separate file, then I can see this being a problem. I think the issue might arise partly from the copy-protection on the DVD -- a common copy-protection trick is to make it look like there are a bunch of identical files, and if you try to rip them individually you'll end up with duplicates, including some possible non-working dupes, and/or an excessively large files. I've even seen movie DVDs were it makes it look like there are a 100 "main features" on the disc, and you've gotta figure out which one is the real, working version of the movie, or you'll somehow end up ripping a 100 gigs worth of bogus files from a 8-gig disc, thanks to the copy-protection tricks. (Note: I think MTR4 is supposed to handle this kind of stuff better than MTR3.)
But what I've been doing for movies and TV-show DVDs is simply using the Mac the Ripper option to rip the entire disc, instead of just the movie or individual episodes. And I keep a shortcut to VLC in my desktop dock bar. Then anytime I want to play a ripped DVD, I just drag the entire folder down to VLC, and VLC opens it up as if it were a DVD . . . From there you can choose the TV episode you want to watch via the original DVD's menu.
It's not the same as storing episodes as individual files, but I've found this to be a faster system for ripping, storing, and watching. XBMC seems to handle the "full disc" Mac the Ripper folders fine as well, at least in "Library" mode -- instead of opening up the folder and drilling down until you find the exact episode/VOB file you want to play, you just have XBMC or VLC or whatever open the top folder as if it were a DVD, and then, boom, you've got your full DVD menu and options and can play the episode/movie/special feature with a single click.
Maybe not the solution you're looking for -- and I'm always looking for better solutions myself -- but thought I'd throw it out there. The method of described has always been super convenient and turnkey for me when I'm just watching the movies on my iMac, but I'm not sure how well it'll work when trying to play back on an Apple TV; that's what I'd really like to know.
(I've also heard that Handbrake can have an easier time of transcoding from Mac the Ripper rips as opposed to using Handbrake directly on the disc -- because Mac the Ripper is cleaning up the copy-protection problems, setting up Handbrake for an easier extraction. Again, I think the idea would be to start with a MTR "full disc" extraction, then run Handbrake on the resulting folder. A lot of people seem to like using both programs hand-in-hand for this type of thing. But I don't have enough Handbrake experience to say for sure -- I'm probably misinterpreting.)