What constitutes a violation of the “nested hierarchy”? Why would a system that is formed by seeded animals that reproduce not form a "nested hierarchy’?
The “nested hierarchy” is a label of the pattern. Were trying to explain a pattern or group of patterns that are not an exact fit to any labeled model.
The alternative question is why the gene sets fit into a dependency graph. You can claim they don’t perfectly as any model is not perfect. Where do we go from here?