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Being away from any testing resources, I assume that Sigil's default NAV is not included in the OPF spine (hence why moving it in Book Browser has no effect in your reading app) and calibre DOES include the NAV in the spine. Both approaches are equally correct. I've just never been a real fan of combining the logical NAV document with a visible html toc, myself. but you're certainly permitted to do so within the EPUB specs, so I don't think Sigil will stop you from manually adding the NAV to the spine if you so choose (again: I cannot test that right now. Someone else may need to fact-check me). It just doesn't automatically do it for you.
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