apple-touch-icon is not a good choice for application icon
If you install a site as a web application, then it Epiphany will prefer an image specified as "apple-touch-icon" for that application. This will result in an ugly appearance as those icons are designed for iOS and forced to confirm to certain quirks there. Most prominently the fact that iOS doesn't handle alpha, so the icon needs to be completely opaque.
It would be much better if Epiphany prefers the standard "icon" instead. Possibly falling back to apple-touch-icon if there are only low-resolution icons.