### 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
ProjectSettings::get_singleton()->save();
			if (file->get_file_mode() == EditorFileDialog::FILE_MODE_SAVE_FILE) {
				save_default_environment();
				_save_scene_with_preview(p_file);
				project_run_bar->play_main_scene((bool)pick_main_scene->get_meta("from_native", false));
			}
		} break;
		case FILE_EXPORT_MESH_LIBRARY: {
			Ref<MeshLibrary> ml;
			if (file_export_lib_merge->is_pressed() && FileAccess::exists(p_file)) {
				ml = ResourceLoader::load(p_file, "MeshLibrary");
				if (ml.is_null()) {
					show_accept(TTR("Can't load MeshLibrary for merging!"), TTR("OK"));
					return;
				}
			}
			if (ml.is_null()) {
				ml = Ref<MeshLibrary>(memnew(MeshLibrary));
			}
			MeshLibraryEditor::update_library_file(editor_data.get_edited_scene_root(), ml, true, file_export_lib_apply_xforms->is_pressed());
			Error err = ResourceSaver::save(ml, p_file);
			if (err) {
				show_accept(TTR("Error saving MeshLibrary!"), TTR("OK"));
				return;
			}
		} break;
		case RESOURCE_SAVE:
		case RESOURCE_SAVE_AS: {
			ERR_FAIL_COND(saving_resource.is_null());
			save_resource_in_path(saving_resource, p_file);