I take an MSWord or any other format manuscript and open it
LibreOffice. All additional needed content for the actual "ebook" is added and positioned... though not cover or sometimes even other graphics. Styles are cleaned up and streamlined.
Using the plugin "
Writer2xhtml", I export the prepared ebook straight to EPUB format. This is then opened up in Sigil for cover addition, tweaking, etc.
I have used multiple layout programs, and things like DreamWeaver, Komodo Edit, etc. etc. I own InDesign and a full Adobe suite and three other packages for layout of traditional publications with export to EPUB as well. I own multiple office suites...
The work flow above is the leanest, quickest, cleanest way to produce purely an ebook and nothing else if that is what you are after. And it's nearly glitch free. I rarely see anything go wrong during validation unless I've personally tried to do something odd. I would not do a pure ebook release any other way, especially since I don't us aggregators and only distribute through direct publishing portals such as KDP, PubIt, WritingLife, etc. And only once as one epub run into a problem due to a slightly non-standard cover image.