That box is really just an optional reference point for a color tinted black. I don’t like using pure black in my interfaces, so I will instead since it toward the primary brand color.
In order to come up with a nice looking color tinted black, I have a rectangle with the primary brand color, then a pure black rectangle on top of it at 90% transparency. More often than not I find that it gives me a nice starting place for color dropping the black that I want to use in the app. You won’t have to make any changes on this rectangle. Use the black rectangle below it in order to set the blacks throughout the system, and if you want, just eyedrop the color from the reference black.
Does that make sense? Sorry, it’s a little bit confusing.