I know this is years later, but I found a solution that might help someone else.
I finally got around to ripping my Blu-ray of this. Neither eac3to nor MakeMKV seemed to find more than the single, stereo-timed chapter from the Blu-ray structure. However, I opened the disc in MKVmerge GUI and was given the option of various playlists. I chose the one with only 11 chapters,
made a CUE file from it, and it's perfect!
Thanks to
Cheezmo and all who explained how there was more than one chapter file in there. I wouldn't have otherwise known to look so deeply.
Attached is the CUE sheet for use with the 5.1 mix, in case it helps anyone.