Code

var ll = new LayeredLayout();
ll.Orientation = MindFusion.Diagramming.Layout.Orientation.Horizontal;
ll.EnforceLinkFlow = true;
ll.Arrange(diagram);

var columns = new Dictionary<int, List<DiagramNode>>();
foreach (var node in diagram.Nodes)
{
    if (!ll.Statistics.NodeLayerIndices.ContainsKey(node))
        continue;
    var l = ll.Statistics.NodeLayerIndices[node];
    if (!columns.ContainsKey(l))
        columns[l] = new List<DiagramNode>();
    columns[l].Add(node);
}

foreach (var column in columns.Values)
{
    column.Sort((n1, n2) =>
        {
            int area1 = (int)n1.Tag;
            int area2 = (int)n2.Tag;
            int areaComparison = area1.CompareTo(area2);
            if (areaComparison != 0)
                return areaComparison;
            return n1.Bounds.Y.CompareTo(n2.Bounds.Y);
        });

    float y = diagram.Bounds.Top + 10;
    for (int i = 0; i < column.Count; i++)
    {
        var node = column[i];
        int area = (int)node.Tag;
        float minAreaY = area * 70; // replace this with your area definitions
        if (y < minAreaY)
            y = minAreaY;
        node.Move(node.Bounds.X, y);
        y += node.Bounds.Height + 10;
    }
}

//diagram.RouteAllLinks();