I'm certainly not an expert on Sigil programming code, but I would hazard a guess that when using the "Add cover" tool it also semantically defines that image as the "Cover" thus identifying it as used. Whereas the plugin doesn't have another way to force sigil to recognize it as being used. I would therefore bet that Sigil is only looking for the <img> tag instead of the <image> tag when determining if an image is being used.
That would be my guess FWIW....but I'll let the smart guys actually look into it!
