I agree. The Mendel Palace cover we have on the site, I made from my manual scan. Did the same for my custom Werewolf cover without the comic book ad. Obviously its more practical to use box scans, but if the manual contains a good full shot of the box art, that can definetly be used too!
In this case I would probably prefer a manual cover scan because I want to make myself a custom NTSC cover for it and I wouldnt have to worry about the hassel of removing all the PAL info on the front. The manual has a pretty clean shot of the full artwork without the mess of all the logos etc. Then I could just rebuild the PAL cover from scratch.