I am currently trying to export a Material ID texture to use with Quixel, however I have been unable to bake the material colors to one single texture as all the colors are a different material on the same mesh. Is this possible?
I tried your problem and came up with this solution. if you are in 2.8 it's easier.
First you create a new UV map for each object that is affected. Then you select all, enter edit mode, this should let them all be in edit mode together, you select all, and unwrap it all to that UV-Map.
Now you create a new Image with your desired resolution.
In the ShaderEditor you add that image to all the affected materials and select it. this will bake the taxture to that image.
Now you make the texture. It all should be now on this one Image.
It worked for me in 2.77? and in 2.8, sure it will work in other versions aswell.