I guess you could use custom CSS to alter the
display:none to hide it, or add your custom background image to that element.
I'm not sure what you mean by the superuser.com page load ? Keep in mind there's a difference between single-page applications like Flarum and standard HTTP websites like Stackoverflow/Superuser. In Flarum there will always be a short time where the header and navigation are shown but the content is still being fetched in the background.