@Kovid - I've spent a number of hours looking into the conversion pipeline in relation to covers... and my head hurts
In particular - the epub_input.py plugin does some "fiddling" to generate a calibre_raster_cover.jpg and associated entries in the manifest along with a "titlepage" entry in the guide. However by the time it gets to the "structure" part of the pipeline, that seems to have magically disappeared and other logic from somewhere has come into play. Whats that all about - I "assume" it isn't just legacy code and actually has a scenario where it makes sense? Perhaps for non epub output or something?
I've found CoverManager being invoked by the epub_output.py plugin at the end, but I'm trying to figure out "what else" is taking place of relevance to covers in between during a conversion. Any other hints you can offer to look at?