My books are edited in RTF for cleanup, then imported into Book Designer for layout, and output as htm. When the htm is placed in Calibre, it's saved as a zip file (by Calibre).
I use Calibre to convert the zip (htm) to epub while setting fonts, chapter breaks, line height, etc. Everything works except the problem with the <body> tag in Extra CSS. Can't get the font name right without workaround as stated in previous posts.