### 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
export_template_manager->popup_manager();
		} break;
		case SETTINGS_MANAGE_FBX_IMPORTER: {
#if !defined(ANDROID_ENABLED) && !defined(WEB_ENABLED)
			fbx_importer_manager->show_dialog();
#endif
		} break;
		case SETTINGS_INSTALL_ANDROID_BUILD_TEMPLATE: {
			gradle_build_manage_templates->hide();
			file_android_build_source->popup_centered_ratio();
		} break;
		case SETTINGS_MANAGE_FEATURE_PROFILES: {
			feature_profile_manager->popup_centered_clamped(Size2(900, 800) * EDSCALE, 0.8);
		} break;
		case SETTINGS_TOGGLE_FULLSCREEN: {
			DisplayServer::get_singleton()->window_set_mode(DisplayServer::get_singleton()->window_get_mode() == DisplayServer::WINDOW_MODE_FULLSCREEN ? DisplayServer::WINDOW_MODE_WINDOWED : DisplayServer::WINDOW_MODE_FULLSCREEN);
		} break;
		case EDITOR_SCREENSHOT: {
			screenshot_timer->start();
		} break;
		case SETTINGS_PICK_MAIN_SCENE: {
			file->set_file_mode(EditorFileDialog::FILE_MODE_OPEN_FILE);
			List<String> extensions;
			ResourceLoader::get_recognized_extensions_for_type("PackedScene", &extensions);
			file->clear_filters();
			for (int i = 0; i < extensions.size(); i++) {
				file->add_filter("*." + extensions[i], extensions[i].to_upper());
			}
			Node *scene = editor_data.get_edited_scene_root();
			if (scene) {