I've ripped hundreds of TV boxed sets and I've rarely seen them with the playlist in any particular order. Worse, I've seen ones where most will be ordered and one oddball isn't. But I've never had an issue. I simply play them in PowerDVD and use Process Monitor to see what mpls it opens (the tool can filter everything else out). This has only ever failed for me on a couple Lionsgate (movie) discs where the Java was smart enough to fool it (I think it's Screen Pass?).
As for commentary in separate tracks, my custom scripting language is able to handle that. I just give it X+Y+...+Z for the title # and it know to extraction all those titles and remux all the tracks into one file (using only the video and chapters from the first). With an option, I can tell it to concatenate them together, instead, for handling movies, et. al., split across more than one disc.
I like to automate as much as possible. Processing Blu-rays (especially TV shows) is laborious!
DrX