Code

void ArrangeContainers()
{
	var innerLayout = new LayeredLayout();
	innerLayout.StraightenLongLinks = true;
	innerLayout.EnforceLinkFlow = true;
	innerLayout.NodeDistance /= 2;

	var outerLayout = new LayeredLayout();
	outerLayout.StraightenLongLinks = true;
	outerLayout.EnforceLinkFlow = true;
	outerLayout.NodeDistance /= 2;

	Arrange(diagram, outerLayout, innerLayout);
}

private DiagramItemCollection GetContainerItems(ContainerNode container)
{
	DiagramItemCollection items = new DiagramItemCollection();
	foreach (DiagramNode node in container.Children)
	{
		items.Add(node);
		foreach (DiagramLink link in node.GetAllLinks())
		{
			DiagramNode node2 = GetOtherEnd(link, node);
			if (node2.Container == container && !items.Contains(link))
				items.Add(link);
		}
	}
	return items;
}

private DiagramNode GetOtherEnd(DiagramLink link, DiagramNode node)
{
	if (node == link.Origin)
		return link.Destination;

	if (node == link.Destination)
		return link.Origin;

	return null;
}

private void Arrange(Diagram diagram, Layout outerLayout, Layout innerLayout)
{
	foreach (DiagramNode node in diagram.Nodes)
	{
		ContainerNode container = node as ContainerNode;
		if (container == null)
			continue;

		innerLayout.Arrange(diagram, GetContainerItems(container));
		container.UpdateBounds();
	}

	outerLayout.Arrange(diagram);

	diagram.ResizeToFitItems(5);
}

static class ContainerExtensions
{
	public static void UpdateBounds(this ContainerNode container)
	{
		if (container.Children.Count == 0)
			return;
		var r = container.Children[0].Bounds;
		foreach (DiagramNode node in container.Children)
			r.Union(node.Bounds);

		container.SetBounds(r, false);
	}
}