### 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
}
			_update_visibility_color(p_node, item);
		} else if (p_node->is_class("CanvasLayer") || p_node->is_class("Window")) {
			bool v = p_node->call("is_visible");
			if (v) {
				item->add_button(0, get_theme_icon(SNAME("GuiVisibilityVisible"), SNAME("EditorIcons")), BUTTON_VISIBILITY, false, TTR("Toggle Visibility"));
			} else {
				item->add_button(0, get_theme_icon(SNAME("GuiVisibilityHidden"), SNAME("EditorIcons")), BUTTON_VISIBILITY, false, TTR("Toggle Visibility"));
			}
			if (!p_node->is_connected("visibility_changed", callable_mp(this, &SceneTreeEditor::_node_visibility_changed))) {
				p_node->connect("visibility_changed", callable_mp(this, &SceneTreeEditor::_node_visibility_changed).bind(p_node));
			}
		} else if (p_node->is_class("Node3D")) {
			if (p_node->has_meta("_edit_lock_")) {
				item->add_button(0, get_theme_icon(SNAME("Lock"), SNAME("EditorIcons")), BUTTON_LOCK, false, TTR("Node is locked.\nClick to unlock it."));
			}
			if (p_node->has_meta("_edit_group_")) {
				item->add_button(0, get_theme_icon(SNAME("Group"), SNAME("EditorIcons")), BUTTON_GROUP, false, TTR("Children are not selectable.\nClick to make them selectable."));
			}
			bool v = p_node->call("is_visible");
			if (v) {
				item->add_button(0, get_theme_icon(SNAME("GuiVisibilityVisible"), SNAME("EditorIcons")), BUTTON_VISIBILITY, false, TTR("Toggle Visibility"));
			} else {
				item->add_button(0, get_theme_icon(SNAME("GuiVisibilityHidden"), SNAME("EditorIcons")), BUTTON_VISIBILITY, false, TTR("Toggle Visibility"));
			}
			if (!p_node->is_connected("visibility_changed", callable_mp(this, &SceneTreeEditor::_node_visibility_changed))) {
				p_node->connect("visibility_changed", callable_mp(this, &SceneTreeEditor::_node_visibility_changed).bind(p_node));
			}
			_update_visibility_color(p_node, item);
		} else if (p_node->is_class("AnimationPlayer")) {