I love Emacs and the auto-fill more. When I work I use it always to make easier to read the text (with a small value, like 80 or 100). Then, if I have to copy to a Word Document (in collaboration with other people) or a text (like in the submission of a review) I simple set the fill-column to a large value (2000 or similar), with C-x f. Later, I copy all the text.