### Godot version

4.0 9f68d06

### System information

Windows 10 x64

### Issue description

When changing any property of tile source, e.g. name:
![image](https://user-images.githubusercontent.com/2223172/219977766-9babbd6c-cd75-41a0-a167-fe6da039d05e.png)
This error appears in the output:
```
UndoRedo history mismatch: expected 0, got 2.
Set name
```
It means that there is an undo action that starts with a global object and continues with a scene one.

Only happens when the TileSet is built-in and it makes the changes to the tileset being registered as global, i.e. not related to its scene (which results in history inconsistency after closing the scene).

I did some debugging and the action comes from inspector, which edits TileSetAtlasSourceEditor and then TileSetAtlasSource. I don't know what exactly triggers it; the properties should be only set on TileSetAtlasSource.

### Steps to reproduce

1. Add scene
2. Add tilemap
3. Add tileset (don't save it to a file)
4. Edit tileset
5. Add atlas source (e.g. drop icon.svg)
6. Change atlas name
7. Observe output

### Minimal reproduction project

N/A
}
			Ref<ConfigFile> config;
			config.instantiate();
			Error err = config->load(EditorSettings::get_singleton()->get_editor_layouts_config());
			if (err != OK || !config->has_section(p_file)) {
				show_warning(TTR("Layout name not found!"));
				return;
			}
			
			List<String> keys;
			config->get_section_keys(p_file, &keys);
			for (const String &key : keys) {
				config->set_value(p_file, key, Variant());
			}
			config->save(EditorSettings::get_singleton()->get_editor_layouts_config());
			layout_dialog->hide();
			_update_layouts_menu();
			if (p_file == "Default") {
				show_warning(TTR("Restored the Default layout to its base settings."));
			}
		} break;
		default: {
			
			if (file->get_file_mode() == EditorFileDialog::FILE_MODE_SAVE_FILE) {
				_save_scene_with_preview(p_file);
			}
		} break;
	}
}
bool EditorNode::_is_class_editor_disabled_by_feature_profile(const StringName &p_class) {