WHAT!!!....lol I just added the custom header and custom background back into my theme. I wanted to make sure that it followed the WordPress guidelines and I figured "Why not, other themes have them in there."

I agree however that these need to be only available in the customizer and cannot wait for the additional links to be removed. I have had so many people ask me what is the difference and when I say they are the same thing, I get the blank stare of doom.

Now if they would just add opacity to the color picker that would be AWESOME!!!