Blender Cycles does not seem to be able to bake textures with any alpha in them whatsoever (unless texture area is unmapped).
I search in the Bug Tracker and find this https://developer.blender.org/rBf3505ab771184877413cfa11336da2ccc1da36ee
It seems any alpha baked in Cycles is pegged to 1.0
Is this expected behavior or have I missed something somewhere?
I’ve tried both PNG and TGA, both with RGBA.
Render -> Film is set to Transparent, so that the World Background is transparent.
My test case is a leaf texture on a flat plane, with nodes like so: http://blender.stackexchange.com/questions/6416/transparent-image-textures-in-cycles
I’ve even tried it with a texture that is completely transparent (it comes out a solid sheet of black).