### 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 (!scr.is_null()) {
			String additional_notes;
			Color button_color = Color(1, 1, 1);
			// C
			if (scr->is_tool()) {
				additional_notes += "\n" + TTR("This script is currently running in the editor.");
				button_color = get_theme_color(SNAME("accent_color"), SNAME("Editor"));
			}
			if (EditorNode::get_singleton()->get_object_custom_type_base(p_node) == scr) {
				additional_notes += "\n" + TTR("This script is a custom type.");
				button_color.a = 0.5;
			}
			item->add_button(0, get_theme_icon(SNAME("Script"), SNAME("EditorIcons")), BUTTON_SCRIPT, false, TTR("Open Script:") + " " + scr->get_path() + additional_notes);
			item->set_button_color(0, item->get_button_count(0) - 1, button_color);
		}
		if (p_node->is_class("CanvasItem")) {
			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));