another reason I have ripped to MKV is that it's very easy, and doesn't require any other software to function. Meaning, i don't own anyDVD HD, and have never used it. So, I don't currently have a way to rip the full file structure, but I believe anyDVD HD will allow you to do this. I have not tested any of the file structure functionality in MC, but from what i have read, it works great. You can point MC to the correct playlist for the different versions and launch whichever version directly; like you can with an MKV file now, more or less.
As for makeMKV, it will let you select whichever streams you like, whichever versions of audio and subtitles and whichever titles offered, like extras and previews. It does not currently give you any useful information about the video/files you can rip, only size and media type, but nothing about titles or versions. i usually rip everything, then delete the crap files later.
It has worked great for me for some time now. The files it creates can be split by LAV nicely, and LAV splitter can detect the forced flags in the regular/full subtitle streams and only present those for you automatically.
However, if you want to keep 2 versions of the movie (theatrical and directors cut), you'll need to MKV files, each full size, so double the disc space. I don't know why you'd want to keep both versions, but you may have to rip both versions with makeMKV, since you may not know which one is which from the data it presents you. simply deleting the 'wrong' one later is easy enough though.
nevcairiel, who develops LAV filters, has indicated his interest in getting some kind of a menu selection system working including edition selection, however, I think it remains pretty far down his list of things to do, and I'm not sure he's ever said he *can* do it, just that he'd like to. I'm sure if it's possible, he can do it, I just don't think it'll happen soon, but have no way of knowing his priorities there.
I've never used tsMuxer, so I can't comment on its usability for this.
hope that helps