Comment by Finnucane

When we get a Word doc from an author it is sent to the typesetter for reformatting. A standard set of style codes is applied and other corrections made so it can be directly imported into the design template. This the version the copyeditor works on. Also: once proofs are set this version is basically trash. In ye olde dayes, when this was all done on paper, the edited ms would eventually go back to the author, but sometimes they didn't want it. Now when the book is done the production manuscript files get deleted.

For ebook production, you could definitely do worse than follow Standard Ebooks' method. That will get you a decent standards-compliant file with basic accessibility features accounted for.