How to bake several textures (including transperent ones) into one diffuse texture?

web

Haven't found any solutions so I decided to ask here, examples are attached below (all of them use only one color texture + normal map)

ZacD

If you're faking it, you can texture and bake the model with complete transparency and with no transparency, bake a thickness texture, and use that thickness texture to blur the texture underneath by depth and control how opaque the top layer is.