### Godot version

v4.0.beta12.mono.official [3c9bf4bc2]

### System information

Windows 10

### Issue description

When using GetTree().ChangeScene (or GetTree().ReloadCurrentScene), the orphan node count in Monitors goes up by the number of nodes in the target scene.

This effect is amplified when running a scene that has lots of nodes.


I've also tested this in the previous beta (v4.0.beta11.mono.official [91713ced8]) and confirmed the issue didn't exist there.

### Steps to reproduce

1. Run the included Minimal Reproduction Project.
2. Open the Debugger/Monitors tab.
3. Press "Space" to load Scene2.tcsn (2 Nodes).
 - Orphan nodes increases by 2.
5. Press "Space" to load Scene1.tcsn (3 Nodes).
 - Orphan nodes increases by 3.

### Minimal reproduction project

[MRP.zip](https://github.com/godotengine/godot/files/10415860/MRP.zip)

_THREAD_SAFE_METHOD_
	ERR_FAIL_NULL(p_object);
	p_object->_is_queued_for_deletion = true;
	delete_queue.push_back(p_object->get_instance_id());
}
int SceneTree::get_node_count() const {
	return node_count;
}
void SceneTree::set_edited_scene_root(Node *p_node) {
#ifdef TOOLS_ENABLED
	edited_scene_root = p_node;
#endif
}
Node *SceneTree::get_edited_scene_root() const {
#ifdef TOOLS_ENABLED
	return edited_scene_root;
#else
	return nullptr;
#endif
}
void SceneTree::set_current_scene(Node *p_scene) {