My issue is simply put: I would like to bake a texture that has some alpha to it (eg, a sheer fabric).
I created an image to receive the bake, with alpha enabled. When I run the bake (combined), the bake has no alpha to it at all (except for whatever lies outside of the UV map). I feel I am overlooking soemthing very basic, but I cannot find it. Any suggestions would be appreciated. 
Thanks anyway.
Hi Miro, i’m having the same problem. I see there havent been any responses to your question, do we need to assume it simply is not possible or were you able to find a solution? Cheers
I found no answers, one way or the others. So I am assuming it isn’t possible.
Anyone found an answer please?
make a material that will use the alpha channel as diffuse, when you bake, make a texture composition node, and use that diffuse texture which was baked to set the alpha. Or simply use the same texture you created the material in the first place to set the alpha of the baked texture.