How to change background color of on an Atlas ?

Obviously the packTextures method doesn't allow to choose the default background color for an atlas, but if anyone as a simple method to do it that would help ^^

Ok i finally found a solution to your (old) problem.
I colorize the atlas after its creation but only the part that have alpha set to 0f like this:

var textureSize = 4096;
Texture2D atlas = new Texture2D(textureSize, textureSize);
var rects = atlas.PackTextures(atlasTextures.ToArray(), 10, textureSize);

var marge = 0.001f;
for (var i = 0; i < atlas.width; i++)
    for (var j = 0; j < atlas.height; j++)
        var pixel = atlas.GetPixel(i, j);
        if (pixel == new Color(pixel.r, pixel.g, pixel.b, 0f))
            atlas.SetPixel(i, j, Color.white);