This might be difficult to implement, but it might be nice if you could label the node numbers in the physical modeler different than used in the analytical modeler so that you could keep those nodes the same. Therefore, they would show up the same in the report. For example, all nodes in the physical modeler would start with a "P".
Thank you for posting this idea. I am trying to understand the motivation and where you are experiencing an issue with the labels? Do you mean in the Physical Workflow or are you looking to see the physical node nodes in the analytical workflow?