### 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
if (p_button != MouseButton::RIGHT) {
		return;
	}
	_rmb_select(p_pos);
}
void SceneTreeEditor::_rmb_select(const Vector2 &p_pos, MouseButton p_button) {
	if (p_button != MouseButton::RIGHT) {
		return;
	}
	emit_signal(SNAME("rmb_pressed"), tree->get_screen_position() + p_pos);
}
void SceneTreeEditor::update_warning() {
	_warning_changed(nullptr);
}
void SceneTreeEditor::_warning_changed(Node *p_for_node) {
	//should use a timer
	update_timer->start();
}
void SceneTreeEditor::set_auto_expand_selected(bool p_auto, bool p_update_settings) {
	if (p_update_settings) {
		EditorSettings::get_singleton()->set("docks/scene_tree/auto_expand_to_selected", p_auto);
	}
	auto_expand_selected = p_auto;
}
void SceneTreeEditor::set_connect_to_script_mode(bool p_enable) {