Ok, that explains it. It really is a mesh viewer rather than a scene viewer. I was just hoping that there is an option for scenes.
Here is the node graph in the inspector:
The Transform nodes are created and then the meshes parented to them, nothing special. The scene is created from parsing a recipe (another 3d standard). That can contain an arbitrary transform hierarchy, so I need to use Transform nodes.
It sounds like Transform nodes would be ignored in general, so grouping everything under a single Transform node would not help. Only mesh transforms may be preserved.
I would be looking for an option in the viewer to use .SceneLoader.Load which may not be a goal for the Viewer as it focuses on nice presentation of single models.
I probably can figure out another way for have a simple scene viewer if Viewer is not targeted that way.