You can check the attached project in which the suggested approach is implemented in button click handler. In the captured video
you can see how I group shapes 1-2-3 and then the layout keeps this configuration. What can be improved in this solution is a specific style for the container shape - so that the Layout will not take into account the hight of the container's Header - this way the group 1-2-3 will be vertically aligned with shapes 4 and 5.
Another solution could be to preserve some shapes' positions (relative or absolute) in a Dictionary, Layout and in DiagramLayoutComplete event - re-create the relative positions of the shapes from a particular group. However, this seems more complicated task and I would suggest using the ContainerShapes' approach - it gives a built-in groping which separates a group of shapes from the entire diagram Layout.
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