An asset can look correct in its source application and still fail after import into Unity. Treat hierarchy policy as a translation problem between tools, with node ownership and parenting and naming checked on both sides.
For Unity, separate source, working, and delivery files. Use stable names for nodes and dependencies, remove unused references, and include a manifest that explains what the downstream user actually needs.
Define which nodes carry geometry, animation, collision, metadata, and reusable grouping before cleaning the scene tree. Apply this hierarchy policy guidance to the actual Unity delivery path.