It seems like that disc actually has two alternate media files on it, 00000.m2ts and 00001.m2ts, they contain the same content, but alternate streams.
00000.m2ts has the streams you are seeing, DTS-HD MA 5.1 and PCM 2.0
00001.m2ts has the missing streams - TrueHD 7.1 with Atmos, and DTS-HD MA 7.1 with Auro-3D
This is a bit unusual but I'm sure they had their reasons - and the menu does it transparently. In MC you can swap between the titles through the OSD as well, or the context menu.
LAV Splitter, which handles title playback, can only stitch files in a timeline, not switch between them on the fly depending on track selection, which is why you only ever get two of the correct titles at any given time on a disc like this.
The AC3 streams are actually sort-of place holders for the tracks they stored in the other file. Which is a bit weird. They are not mis-identified, and are not a lossy base for the Atmos stream or anything of that sort.
All other analysis above are unfortunately just pure speculation and ... wrong.
If all streams actually play through the menu in MC, I'm a bit proud.