From looking at the underlying code in the user guide pages --- it looks as though Cover.html is simply an .html page containing the cover image.
Cover_picture.html also contains the cover image, and is linked to the CSS stylesheet, PLUS has a heading that allows it to be added into the auto-generated Table Of Contents.
Code:
<h1 class="nodisplay" title="Cover"> </h1>
Cover.html might be superfluous, but I haven't read through the guide carefully either. Maybe it is used as an example in the section on adding covers.