### Godot version

3.5.2.stable, 4.0.1.stable

### System information

Arch Linux

### Issue description

When the `Show Hidden Files` property is enabled in the Editor Settings:
![image](https://user-images.githubusercontent.com/6501975/226908540-8e70e520-3dcd-46e4-beaf-103ac176c1de.png)
Any `FileDialog` nodes from the project will inherit this setting, and their `Show Hidden Files` property is set to true everytime the scene is re-opened:

https://user-images.githubusercontent.com/6501975/226909135-a8fafdf7-ca36-40aa-b69a-a7baf2d7ae4f.mp4


This occurs on 3.5.2 as well.

### Steps to reproduce

- Enable `Show Hidden Files` property in the Editor Settings:
    - Reload Godot for the bug to occur
- Create a FileDialog node, and set it's `Show Hidden Files` property to false
- Save and close the scene, and reopen it
- The `Show Hidden Files` property is reset to true.

### 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) {