Does dot's solver ignore layers?

I would like to use layers to allow some nodes/clusters to be on top of others. However, the solver/optimizer still seems to be trying to keep them from overlapping.

Note that I have some nodes appearing in both layers, as "connectors" which must remain lined up.

Is it possible to do this purely with layers, or should I generate a graph, fix the position of the connectors, and then break out the nodes into new graphs and do a second optimization pass? I'd like to avoid all that extra work if possible.

I can provide specific examples if needed.

-Max E.

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