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If you select them, they get included. If you don't, they don't.
It doesn't look at any <guide> tags, if that's what you're asking.
If the source book has a cover in calibre, it will copy that to the new book record before presenting the metadata. If there's a cover in the metadata after it's been presented and accepted (from the original, downloaded, whatever), it will be included in the EPUB.
No other html files are given any special consideration.
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