@stumped - what you see in the library (book details, cover grid etc) has nothing to do with what's in an ePub file - its simply a bitmap display of the cover.jpg file in the book folder, no more, no less.
If you use library functions such as conversion, polish, modify, embed metadata, send to device and save to disk, some of them can take the file 'cover.jpg' in the book folder and put it into an epub (or other format files), wrap it in a barebones titlepage.xhtml, and update the content.opf file accordingly. Any subsequent customisation made within the ePub itself to the titlepage and/or the cover image are local to the ePub.
BR
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