Well, you can create a two-level ToC.
The Book-level nodes will display with the chapter-level nodes collapsed.
The NCX usually shows in a special navigation sidebar/popup/dropdown.
This is often seen in omnibuses. Like the one you are asking about.
Nothing wrong with omnibuses. I
personally prefer splitting them with EpubSplit (calibre plugin). But some people like squashing them together with EpubMerge!