This is for the moment not possible the auto-layouter should do it's work in your case it's seems not. Is it something 100% reproducible? Could you share with us a script that produce such output so we can fix the bug? Moreover for moment this is not possible to define the node position on a graph node. I forwarded this request to the responsible development team, but there is no guarantee that this will be implemented.
The data dictionary can be used to define default parameters value by passing a NodePath before it's creation but the semantic is a bit complex in Python so I would advice you to use
SetDefaultValueonce a port is created as demonstrated in Modify Node Graph Example.