When I play the disc on my PS3, I get the DTS-HD Audio just fine. And the commentary track as a selectable option. All OK.
Popped the disc into MakeMKV for my usual backup ritual... and surprisingly only the main DTS-HD track shows. The commentary AC3 track is completely non-existent.
Opened up tsMuxerGUI and voila! Everything is there. Under the very same .mpls file.
Below is a screenshot of what I see:

I'm using the latest Beta 1.8.8; and the result is the same on 1.8.7 by the way.