See:
https://github.com/kovidgoyal/calibr...7efbd33114fb79
calibre should now support
making both NCX and Nav ToCs for EPUB3, in order to maintain wider compatibility.
However, the Viewer itself will still expect to see a proper EPUB2 ToC in NCX format, which is understandable since it is an EPUB2 viewer.
...
Apparently, it is okay for calibre to get a certain limited amount of EPUB3 support, or perhaps Kovid just doesn't want to break existing books.