I think running combineChildren on the individual tree/branches THEN try parenting them as a child of a GO and regenerate the static batching. You could also create a new prefab runtime (I think) before adding them to the static world

eg

GameObject newThing = (GameObject)Instantiate(thingToSpawn, position, rotation);
newThing.isStatic = true;
newThing.transform.parent = root.transform;
// Spawn everything else too

StaticBatchingUtility.Combine(root);