I am trying to remove the widgets from the header area. But somehow…. they don’t show in customizer. The area where they should be is all grey and weird?
If you don’t want Header Widget Areas then you can disable it from Customize > Header > Widgetbar > Header Widget Areas. Certainly it’s there and you need to set “None” – http://prntscr.com/e9rqkt
I have set it for you as you seems struggling to find this.