I thought you would be able to just setup the scene-graphs in the resource layout.
It would then save the data and be available in the rest of the project similar to when you want to setup object variables for a project.
Reading DiegoM post i realized Construct doesn't really have a scene-graph "entity" with all information incorporated. Instead we have the parents with the info of their children, and then the children with the info of their applied transforms.
Hoping that what he is planning to implement will allow something similar to setting up the objects on the editor, pick one of the objects and allow to save the info of all connected objects to a json.
Then at runtime you would be able to load the json and create the objects and connections it describes.
Maybe create one of the objects at the expected position and then be able to "inject" the json information.
Another aproach would be to "upgrade" containers to allow setting and saving the relations of it's objects like mikal tried?
(though you would have to keep single objects for similar parts with different positions/connections since it doesn't allow duplications)