It's been a while since I touched SpeedTree, but I remember they used a whole lot of UV channels (7-8). I think they just blend different channels using vertex colors (or alpha), plus of course adjust the normals. Certainly there are no additional alpha textures other than the detail texture with alpha.
Just to give a good idea about what kind of data is being stored in your geometry when exporting /w certain features enabled in SpeedTree. If you arent going to use the branch blending features, you could try adjusting the "Light Seam Reduction" property to affect the normals of the branch you want to blend, there is also…