Child node is duplicated incorrectly when instancing and adding a scene(which inherit another scene) to the scene tree through editor plugin

[univeous]

Godot version

3.3.4.stable

System information

Windows 11 21H2

Issue description

I know the title is a little unclear and awkward, but I will try to explain.
Let's say there is a scene A:

and scene B inherits A and has its own children:

If we instance and add a B scene to scene tree through editor plugin:

tool
extends EditorPlugin
…
	var node = load("res://Node2D_inherit.tscn").instance()
	#assume one node is selected.
	get_editor_interface().get_selection().get_selected_nodes()[0].add_child(node)
	node.set_owner(get_editor_interface().get_edited_scene_root())
…

If I right-click the newly added node and check "Editable Children", then save the scene and open it again, strange things will happen:

Some children of scene B are duplicated.
This seems only to happen with a scene that inherits another scene. If change the code to make it instance and add scene A, everything seems fine.

Steps to reproduce

Open the Minimal reproduction project, select the root node, click the "Add Scene" button in the canvas editor menu:

Right-click the newly added node and check "Editable Children", then save the scene, close it and open it again.

Minimal reproduction project

EditableChildren.zip

[kleonc]

Duplicate of #49660, it's fixed since 3.4.beta5 (389e67a).