Precise position of nodes with nested clusters

[viharm]

I've recently created a diagram where I needed to precisely position each node to explain what I'm doing. This answer #243 (comment) from @clayms really helped, as switching to the neato engine, and then using the pin and the pos properties for the nodes really allowed me to perfectly position the nodes.

However this has resulted in me losing the grouping of the nested clusters. All my nodes are visible and correctly positioned, but they are no longer visually grouped by the cluster definitions. Only the top level cluster is visible.

I also tried the fdp layout engine, but I lose node positions in favour of nested clusters.

Is this a limitation of the neato method? Or is there a setting I'm not seeing.

I'm sorry if this has been answered elsewhere (as I'm sure this is a popular approach).

I'm also always struggling to mentally link diagrams.py to Graphviz, which makes it difficult to try out various Graphviz settings.