You can do episodic DVDs with the new version.
Just rip the complete DVD to your HDD, process with IfoEdit to remove unwanted audio and subtitle streams, then re-encode with DVD2One. When finished, join the new files overwriting the contents of the original.
Works like a charm on Buffy the Vampire Slayer, 24, MASH, and Friends.
Haven't had a chance to try my X-Files discs yet but I will. I believe they span more than one VOB set - process shouldn't be too different though.
I can give more explicit instructions if needed.