I got tired of continually jumping into an image editor to take a specular map and put it in the alpha channel of my diffuse so that some shader would be happy. So I created this simple substance that does it for you. All it does is take the alpha of one texture and place it into the alpha of another. Usage is simple. Unzip the file and import the substance into Unity. Then put the texture you want to take the RGB value from into the RGB texture slot, put the texture you want to take the alpha from into the Alpha texture slot, pick your resolution, and use (or export) the generated texture. "But the alpha I want is in an RGB texture and not the alpha channel!" you say. Not a problem, just check the "Generate alpha from grayscale" checkbox in Unity's texture importer to push the grayscale value into the alpha, then use the substance normally. Hopefully this helps some people out.
I know this is a very old thread, but I was just looking for a solution to this and this one is awesome! Thanks.
Hey I just found this and its Great. If you want you can use the Alpha Merging Substance with substance player, simply open substance player, browse to where you have unzipped the alphaMerger sbsar file. drag your diffuse image and load into the RGB slot, drag your alpha and load into the alpha slot. choose your size and export. Very handy indeed thanks to the creator