I'm a recovering English teacher, so I know the basics. Still, every publisher has a formatting guide, and NONE of them agree on how one must submit work. So, no matter how carefully an author sets up a MS, there's a point where she must go back and "fix" the things the publisher wants done another way. To quote Robert Frost, "It couldn't be called ungentle, but how thoroughly departmental."
Ellipsis: space before and space after, or no?
Quotation marks around a phrase at the end of a sentence: inside or outside end punctuation?
Em dash: two shorts or a long, with spaces or without?
Chapter headings: bold, all caps, all tiny caps? Numeral or written word for the number?*
And so on, and so on. Who knew publishing could be so much fun?
*Hint: Don't answer these questions, because you'll only be correct for your publisher, not mine!