Perhaps I have not explained clearly.
When you select a texture and open Atlas maker, I can click on Add/update to include selected texture into atlas.
When this happens, the texture import setting changes , but I would like the import setting to have "Alpha Is Transparency" option checked on as well.
At the moment , resulting atlas is correct, but the texture import setting is such that it's transparency is not visble in Unity. We use these textures somewhere else as well.
It doesn't matter if my scene setting is 2D or not.