I believe this direction is leading towards detaching the whole Appearance menu from the Dashboard and ultimately becoming the Customizer. It somehow gives us the restriction in the future indeed but freedom can be chaotic and limiting in some ways. Now, dashboard can be a place of turmoil or pandemonium.

Customizer can be the baseline as to how developers/users should manage to add options to site's layout and style.

Dashboard has to change. Even if this powerful thing we love so much is an open source - it should conforms to some sort of collaborated guidelines.