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At least on the Kindle, where you start is controlled by the "Text" attribute in the <guide>, Sigil has a semantics menu in the file browser.
However, the Kindle does not consider the cover.jpg to be "part" of the book. You can always add a cover.xhtml in addition to the cover, and set that to "Text",but then you will have two cover images which doesn't look good.
I have no idea about iBooks.
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