For this one, issue is with the save and run button. When you change the engine name and click on save & run button. the engine name is not being updated. It only updates when the save icon is clicked.
This method Dynamo/src/Libraries/PythonNodeModelsWpf/ScriptEditorWindow.xaml.cs at master · DynamoDS/Dynamo · GitHub doesnt update the engine name and originalScript like the save() does. Don’t think this is an issue with IronPython3.
Created a JIRA task for these: https://jira.autodesk.com/browse/DYN-5862