There's one less chapter because the BD has a chapter to mark the end, which MakeMKV removes.
Educate me here, I've opened Supernatural S1D1 with Clown BD, all the subtitles are listed in the main mpls listing and the SubPath only contains a few "interactive graphics" that TSMuxer can't rip. I can't find any instructions for the program but I have found mention that things that appear in the main listing are removed from the Subpath.
I don't know this program, maybe you know what's happening better than I do, but to me it looks as though the subtitles are listed in subpath for the reason that they're not actually referenced anywhere else, which would mean MakeMKV and ClownBD are telling you pretty much the same thing...
???
One thing I find interesting though is that ClownBD seems to have merged the Region A + B title stats.
I assume T_SUBTITLE means "Text Subtitles", every BD I've ripped has had PGS subtitles, I'm not sure MakeMKV can rip Text. Is this an actual commercial disc?
According to wikipedia:
DVD and Blu-ray only differ in using run-length encoded graphics instead of text
but it also has:
AUXDATA directory: contains Sound data files and Font files. sound.bdmv file: stores data relating to one or more sounds associated with HDMV Interactive Graphic streams applications. This file may or may not exist under the AUXDATA directory. If it exists, there shall be only one sound.bdmv file.
aaaaa.otf file: stores the font information associated with Text subtitle applications. The names of these files are in the form “aaaaa.otf”, where “aaaaa” is a 5-digit number corresponding to the Font
Hmmmm.