Since WordPress 4.7, the customizer provides natively a free CSS editor (see release post). The first idea was to remove the CSS editor form the plugin, but…

The newly implemented CSS is attached to the current theme, it means that if you change your blog’s theme, the custom CSS will be reinitialized. It’s fine since the look of your blog is mostly dependent of your theme. So it make sens to keep an alternate editor, cross theme, where you can set fine CSS rules related to plugins.

How we managed it in version 1.7 :

• To avoid confusion, the controller has been renamed into “Global custom CSS”.
• All controllers (Addons, Libraries and Global custom CSS) has been moved into the new customizer section “Custom CSS”

So, the customizer panel is still consistent.