For epub3, you have no choice in including the ToC as an xhtml file since that is what the epub3 spec uses as the
mandatory navigation document. You can hide the navigation document from displaying by controlling whether it is in the spine. I've done this on a couple of occasions when a overly fancy (IMHO) html ToC has been wanted.
For a cover page, I use one with an SVG wrapper and remove it for times when the book is being sent to Amazon.