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For #4: epub3-itizer created the nav at OEBPS/nav.xhtml and BookBrowser displays it inside the Text folder which I find misleading.
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No, as I tried to explain. Each folder in BookBrowser shows virtual groupings of files. So no matter where nav.xhtml is physically located in the epub, it will always show up in BookBrowser in the "virtual folder" that represents Text (application/xhtml+xml media types).
Again there is no recommended or constraints on epub3 layout. There need not be a physical folder called Text at all or there could be multiple physical folders called book1 and book2 or ...
So to work with all files of a single type by multi-selecting, the files must appear as "contiguous" in BookBrowser no matter how they physically laid out.
That is the role of BookBrowser. Real book paths can be enabled if you care. Or you can move things around to make physical folders to match the virual folders (standardize it like old Sigil did).