I'm afraid I dont keep the details of cover handling in my head. I'd have to trawl through the code myself. IIRC the idea is that epub input creates a raster cover and a reference to the html cover (removing it from the spine), if the html cover is defined in the metadata. The rest of the conversion pipeline does nothing with covers, the various output plugins either use the raster cover, or for epub output do something complicated like replacing the html cover or adding one depending on the cover situation in the input document.
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