The assignment to levels depends on the setting for "Layer Assignment Policy" in the Layers tab and the structure of the graph. Note that all of these policies except "From Sketch" strive to minimize the number of layers. Therefore, nodes with similar edges are placed in the same layer. In your case, if all "tower" nodes have only edges to the top-level nodes, all tower nodes will be placed in the second layer.
The only way to prevent this is using the "from sketch" setting.