Padding between cluster boundaries and nodes when using Graphviz and neato

I want to generate the following graph in Graphviz:

For reasons explained here, this:

digraph
{
   layout=dot;
   rankdir="LR";
   overlap = true;
   node[shape=record, height="0.4", width="0.4"];
   edge[dir=none];

   A; B; C; D; E; F; G; H; I;

   A -> B -> C;
   D -> E -> F;
   G -> H -> I;
   edge[constraint=false];
   A -> D -> G;

   subgraph clusterX
   {
      label="Cluster 1";
      A; B;
   }

   subgraph clusterY
   {
      label="Cluster 2";
      E; F; H; I;
   }

}

produces this:

Following some careful tweaking of the order of appearance of nodes:

   F; E; I; H; D; G; A; B; C;

I get the correct result.

While this works, I would like more direct control over the placement of nodes, so I tried switching to neato so that I can force the node locations using pos:

graph g
{
   layout=neato;
   node[shape=record, height="0.4", width="0.4"];
   edge[dir=none];

   A [pos="1,3!"];
   B [pos="2,3!"];
   C [pos="3,3!"];
   D [pos="1,2!"];
   E [pos="2,2!"];
   F [pos="3,2!"];
   G [pos="1,1!"];
   H [pos="2,1!"];
   I [pos="3,1!"];

   A -- B -- C;
   D -- E -- F;
   G -- H -- I;
   A -- D -- G;

   subgraph clusterX
   {
      label="Cluster 1";
      A;
      B;
   }

   subgraph clusterY
   {
      label="Cluster 2";
      E; F; H; I;
   }
}

This gives the following result:

How can I get neato to add padding between the cluster boundaries and the nodes within the cluster (in the same way that dot does)?

I hate to be a party pooper, but I don't think the neato-with-fixed-positions-and-clusters approach will be successful.

Cluster support depends on the layout engine - not all engines support it to the same degree:

Note that, for good and bad, cluster subgraphs are not part of the DOT language, but solely a syntactic convention adhered to by certain of the layout engines.

Neato does not seem to be a part of the engines supporting clusters, and while fdp does support neato like layout, it does not support fixed positions.

In the above linked forum entries, ERG proposes at some point to use a gvpr script to achieve this - probably not the solution you had in mind.

By the way, the graph should not be a directed graph, I get warnings and replaced all -> with --.