I spent a couple of hours today figuring out how to create smooth biome color boundaries in my animations, and this is my first test:
Method for creating the biome boundary:
Before I could create a foliage transition, I needed to create a new material for the foliage. To do this, I separated all of the faces in the scene that contained foliage materials. I even included the dirt faces to make it more consistent with the rest of the biome. I decided not to include water, and used a completely different material for it.
I created a texture map of the colors in a biome using an image editor, then I went into orthographic mode and viewed the scene from above. I then created a new uv map for the foliage object and unwrapped using my perspective on the scene. I used the uv map on the biome map texture that I had made and mixed it with the RGB of the original terrain textures before using the alpha of the original textures to create transparency.
This image also has a compositing setup similar to what I used in my most recent animation.
This is the biome map texture for those who might be curious: