They talk about multiple colors during those other threads. The information is probably a tad bit outdated, but the basic gist of it is that the Civ Colors will be set to overlay your flag no matter what you do, based on the alpha layer.
White in the Alpha Layer is Civ Color 1, Black in the Alpha Layer is Civ Color 2. So you need to specify for one of the Civ Colors to be very high Alpha (so that it won't obscure the image you want to create on the flag), and then set the alpha layer to use that color for the entire flag.
Other than that, you just have to live with having some color washed over whatever image you are placing on the flag.