Hello,
You can do anything you want, basically, as long as you leave the SpeedTree node intact in the material.
When you import a SpeedTree, the vertex color is only used for the SpeedTree-baked AO value. It has nothing to do with wind. But if you are exporting a tree to Maya or something, painting a vertex color, and bringing it back into UE4, you’ll lose all the vertex data that does pertain to wind.
To do the blend like your picture shows, you could just use the vert’s Z value in an interpolation between two colors. If you wanted to do something fancier, you can set up detail texture coordinates in the SpeedTree Modeler to put an additional texture on the trunk.