Steps to reproduce:
1. Load scene "Lightmap01"
2. In menu Window->Lightmapping
3. In a window press "Bake scene"

When I bake lightmap, the models that use substance material with a transparent shader dont get the shadow transparent in the lightmap based on the texture, the opacity is ignored on the lightmap how you can see on the image attached. I've tried use a unity material with the substance texture but the problem continue...