Baking textures doesn't use alpha

I work in the game industry and i love to bake textures from HighPoly / PC to LowPoly / Mobile.

Some models use alpha in their textures like hair carts or ripped cloth. Blender doesn't take in account the alpha of a texture so you just get the texture without alpha baked on the new mesh.

Here is an example:

If you want to bake this into a plane:

This is the result you will get:

You will not be able to see the rest of the layers because alpha isn't taken into consideration.