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 https://github.com/DynamoDS/Dynamo/blob/master/src/Libraries/PythonNodeModelsWpf/ScriptEditorWindow.xaml.cs#L457 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