Thanks guys.
A post release thought I have had is that in the next release I will change the check for unmanifested files. By definition currently it is a superset of the bookmarks and plist files, plus any other "stray" files you may have hiding in your epubs.
Instead I think I should make it a check for "other" files excluding plist and bookmarks ones. That way if you decide to for instance retain Calibre's ability to open an epub at the last page read in its ebook viewer, you could still detect other stray files lurking within with this check.
@Idolse - I think that is two of the four items off your checklist you posted
here. The other two items you mentioned were checking for embedded fonts in the opf file, and checking for svg files. If either of these is simple to describe in a PM let me know. Or if you want to code them yourself to send to me then take a look at check_epub.py where all the ePub checks are, and the top of config.py where you define a menu item.