How to fix: SpeedTree Leaves and Bark using same material.

I create a tree and use a leaf texture for leaves and bark texture for the trunk and branches. I save it as a prefab. When I load a scene, the textures have merged, with the leaves being bark texture with a leaf texture on top. When I try to fix it by reassigning the texture, it makes both the branches and leaves either the bark texture or the leaf texture. How can I fix this nonsense? Is this a Unity 2017 bug?

You can fix that issue by making sure you save the tree from SpeedTree as an LOD. Then, when in Unity, you can go to the models under the GameObject that holds the trees, and you can change the materials individually under the Material Elements for that model in the Inspector Settings.