I'm not sure if there's anything special about configuring a fallback ncx in epub3, but regardless ... I can't imagine that the ncx would be listed as an itemref in the spine—linear or no.
I'm pretty sure a fallback ncx is handled just like an ncx in epub2 --
In the manifest:
<item id="ncx" href="toc.ncx" media-type="application/x-dtbncx+xml"/>
and the spine:
<spine toc="ncx">
<itemref idref="cover" linear="no"/>
<itemref idref="book" linear="yes"/>
<itemref idref="toc" linear="no"/>
</spine>
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