it's only one small part, but removing the NES logo rectangle would leave an empty space that needs to be filled in with the original image.
let me show you here..

i mean, it could be done without the original, by re-drawing it by hand, but that would take unnecessary work that i personally don't feel like doing. whoever made the cover likely has the original image still underneath the rectangle layer, so all they would have to do is delete that rectangle and pop in the ultra logo. easy, easy.