### Godot version

4.2 6da4ad1

### System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

### Issue description

![image](https://github.com/godotengine/godot/assets/2223172/d65ab202-93dd-4d83-bcef-c2b34bfa23f3)

In 4.2 dev3:
![image](https://github.com/godotengine/godot/assets/2223172/8621ec24-65d4-490d-bfc1-7e6e8aa3606a)


### Steps to reproduce

1. Create a scene with some children
2. Instantiate it in another scene
3. Enable editable children

### Minimal reproduction project

N/A
tree->connect("multi_selected", callable_mp(this, &SceneTreeEditor::_cell_multi_selected));
	tree->connect("button_clicked", callable_mp(this, &SceneTreeEditor::_cell_button_pressed));
	tree->connect("nothing_selected", callable_mp(this, &SceneTreeEditor::_deselect_items));
	error = memnew(AcceptDialog);
	add_child(error);
	warning = memnew(AcceptDialog);
	add_child(warning);
	warning->set_title(TTR("Node Configuration Warning!"));
	last_hash = 0;
	blocked = 0;
	update_timer = memnew(Timer);
	update_timer->connect("timeout", callable_mp(this, &SceneTreeEditor::_update_tree).bind(false));
	update_timer->set_one_shot(true);
	update_timer->set_wait_time(0.5);
	add_child(update_timer);
	script_types = memnew(List<StringName>);
	ClassDB::get_inheriters_from_class("Script", script_types);
}
SceneTreeEditor::~SceneTreeEditor() {
	memdelete(script_types);
}
/******** DIALOG *********/
void SceneTreeDialog::popup_scenetree_dialog() {
	popup_centered_clamped(Size2(350, 700) * EDSCALE);
}
void SceneTreeDialog::_show_all_nodes_changed(bool p_button_pressed) {
	EditorSettings::get_singleton()->set_project_metadata("editor_metadata", "show_all_nodes_for_node_selection", p_button_pressed);
	tree->set_show_all_nodes(p_button_pressed);
}
void SceneTreeDialog::set_valid_types(const Vector<StringName> &p_valid) {