Very interesting, Man Eating Duck.
Our situation and workflow is very similar to yours, apparently. Except, we're still using CS4, so I have to manually change the chapter header styles from <p to <hx ( and insert sigil_split_markers at the same time).
CS4 stylesheets do give measurements in em's, so that's not a problem (but color is). We use standardized style names across the print and ebook versions, so it almost matches up automatically (modulo things like dropcaps etc.).
I just deal with the cover image and metadata directly in Sigil. Specific metatdata is supplied by the publisher in a separate text file, and I copy and paste into content.opf directly. Calibre sometimes adds things I don't want (or used to) so I stay away from it for commercial projects.
We deal with images and embedded fonts the same way you do.