Forest handles all geometric objects as a collapsed meshes. But really, although the plugin would to preserve the instanced branches, there are not benefits doing this, because all scattered objects of a same type are identical for the renderer (they are instances).
Why do you want to preserve the instances hierarchy, to create diverse samples of a same tree or something else ?
On the other hand, you can use a Forest object as source geometry for another Forest object, setting the Display->Mode parameter of the inner object to "Meshes" (the default value is "Auto"). There is a grass sample scene using this technique in another post in the forum.