So I tried a few different answers that I found here, and I feel that this is possibly a duplicate question, but everything I have tried from the other solutions hasn't worked.
Basically I am trying to bake a material to a texture that will be used in Unity, but every test gives me a black background image.
In the image below, the top image texture is the mask (black and white, white being the leaves), and the bottom image texture is the colour.
It is currently not possible to bake directly to an alpha channel as you mention.
https://blender.stackexchange.com/a/41904/28015
There are workarounds, though, like you could bake only an emission shader of the masking (in this case you already have the mask so there's no need for that), then make it the alpha channel in the compositor.
Here is the blend:
Just bake the texture, update the compositor, and finally, go the the viewer node in the uv editor.
What you should do is, creat a new texture in the uv/image editor and change the color from black to transparent by sliding the alpha value. Then in your baking menu disselect clear. This now should give you your leaf with a transparent background once you've baked it.
I don't know if this can help you, but what works for me is this. I did 2 bake textures, 1 the regular bake texture, and the other is just a glossy bake type, only the color and that created a B&W image that then you can use as a mask in photoshop... 
