You have added the ability to add a header widget, which is great for adding things like phone numbers etc. However there is nothing in color settings to allow for color updates, only settings for sidebar and footer widgets. I am guessing this could be also needed for presentation page columns?
The header widget is a very non-standard header area. There is no default content that can always be placed there and most people will add their own HTML (most likely via the Text Widget) and will need to use their own CSS to style that HTML. The theme’s (theoretical) built-in colour options would rarely be useful in this case scenario.