I haven't done detail; work with cookies, but have with molded chocolates. I would make milk/powdered sugar glazes of desired colors, using paste food coloring, and a fine-tip brush, or dental spatula to apply the colors. You will need multiple, food safe paint brushes, or a paper towel to clean the spatula between colors.
Detailing work, whether piping icing, or painting on glaze, is time intensive, not really great for mass production. It's easier, and faster to simply dust edible glitter, or colored sugar on top.
Another option would be to make a large, baked cookie, on a sheet pan, paint the inside of the cookie color with the appropriate glazes, and the use it to cut the cookies. I would think the colors would be pressed into the cookie details.
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