I can duplicate the issue. It only affects EPUB3s. I
see it, but I don't know how to fix it yet. Just "seeing it" is a huge part of the battle for me, though.
Thanks for the bug report and the details.
P.S. the code in place is definitely intended to allow you to replace an existing cover, so it's not just a "lazy" thing.
It's just missing a piece that removes the properties="cover-image" portion from a previously existing cover image with EPUB3s.