### 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
int scene_idx = (current_menu_option == FILE_SAVE_SCENE || current_menu_option == FILE_SAVE_AS_SCENE) ? -1 : tab_closing_idx;
			if (file->get_file_mode() == EditorFileDialog::FILE_MODE_SAVE_FILE) {
				bool same_open_scene = false;
				for (int i = 0; i < editor_data.get_edited_scene_count(); i++) {
					if (editor_data.get_scene_path(i) == p_file && i != scene_idx) {
						same_open_scene = true;
					}
				}
				if (same_open_scene) {
					show_warning(TTR("Can't overwrite scene that is still open!"));
					return;
				}
				save_default_environment();
				_save_scene_with_preview(p_file, scene_idx);
				_add_to_recent_scenes(p_file);
				save_editor_layout_delayed();
				if (scene_idx != -1) {
					_discard_changes();
				}
			}
		} break;
		case FILE_SAVE_AND_RUN: {
			if (file->get_file_mode() == EditorFileDialog::FILE_MODE_SAVE_FILE) {
				save_default_environment();
				_save_scene_with_preview(p_file);
				project_run_bar->play_custom_scene(p_file);
			}
		} break;
		case FILE_SAVE_AND_RUN_MAIN_SCENE: {
			ProjectSettings::get_singleton()->set("application/run/main_scene", p_file);