My theory on ecosystems, is that if you notice in the plant editor there are parameters for change the look of a tree. I believe that ecosystem has a single instance of the object which is procedural object and for each variation of tree, it applys a slight different variation. Also rotates the object on the surface. If you read the manual, you notice that if you save an rock as vue object and include it ecosystem, it will also have different variations. If you decided to export an rock to another format, then you would likely only get scaling and rotation on the object. Very similar to XFrog or Poser objects in an ecosystem.