Which, loops all the way back around to your initial question. You should rip the "one with chapters" ie the playlist (mpls).
The situation was just as I suspected:
Glad you're all sorted out now! Good luck.The content on a BD/UHD listed out by MakeMKV are either playlists, or individual m2ts files. A playlist, does exactly what it sounds like, it is a list of files (m2ts) to play and in what order.
In the case of the Halloween disc that you have in your screenshot, the playlist file (the one with chapters) is likely comprised of just one m2ts file. So the content wouldn't be duplicated. All the video and audio data is stored in the one m2ts file.