The option text is interesting:
Quote:
--remove-first-image
Remove the first image from the input ebook. Useful if the input document has a cover image that is not identified as a cover. In this case, if you set a cover in calibre, the output document will end up with two cover images if you do not specify this option.
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So that implies that if the cover image is detected (it is, at least in get_metadata) there should be no duplication. In result the question is: if the cover image is detected, who will remove it from the resulting xhtml in the input process? (if it is not some meta information but real markup)