Bring it on, Milkweed! I would like to see that article. I think getting into layers is a basic step toward permaculture and thinking vertically you can even do it in a whiskey barrel.
But I think, unless all you have is a 10th floor balcony, that you can get into all kinds of horizontal complexities, too. One thing I noticed growing up in the a Northern Michigan maple-beech forest, is that a naturally growing woods is far from homogeneous. There are the edges, the meadows, the wet areas, the conifers, the deciduous trees, and the fruiting srubs and trees, not to mention the wildlife that is part and parcel of a natural ecosystem.
I think the food forest concept and Bill Mollisons idea of zones takes this horizontal dimension into account.