[kovidgoyal]

The EPUB specification has no well defined concept of a cover. In EPUB the "first screenful" is the cover. To work around this limitation, most ebook processing systems use a custom tag in the OPF that points to an image identified as the cover. In addition some epubs use an item in the guide to point to an HTML file as the "titlepage". In this case the first screenful (usually rendered at 800x600) is taken as the cover. In both these cases calibre can manipulate the cover. In the former it just replaces the image pointed to by the custom tag. In the latter it replaces the entire HTML file pointed to by the titlepage item.

However, if neither of these is present, there is no way to be sure that the first HTML file contains only the cover, so it cannot be safely manipulated.