One way to fill whole areas of a flattened image with a color is to select the areas you want filled, make the color you want those areas filled with the Background color, and choose Edit...Clear (or hit the Delete key) - the selected area(s) will be flooded with the Background color. The background color is always used in this process (the one showing in the Background Color box), even if a gradient or pattern is selected in the Background Material box.
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