WordPress theme developers will be pleased to know that the upcoming 4.1 release will remove the custom background and header screens in the admin. These screens will be replaced with deep-links to the customizer. To be clear, header and background menus will still appear in the admin, but they will be deep-linked to the customizer.
This is good news for WordPress theme developers, because they will no longer have to style the custom header and background screens.
@devinsays Finally. I hated styling the Custom Header screen. Good riddance!
— Justin Tadlock (@justintadlock) November 20, 2014
The key issue to consider is whether hiding these pages will cause issues for updating users. New users actually tend to have trouble with the separate headers page, expecting that functionality to be in the customizer.
Header upload was pulled out of the customizer in WordPress 3.4, due to issues with cropping header images. For the past two years, the extra admin pages were confusing for users. With some theme controls in the customizer and others available in the admin, the experience of customizing themes was inconsistent and divided between the front and back ends.
Changes coming in 4.1 will replace the custom background/header screen links in admin menu and toolbar with deep-links to the customizer on the frontend. The widgets screen will also display a link to the customizer widgets panel. In the future, the plan is to remove these admin links entirely in favor of streamlining everything to the customizer.