### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

if (err != OK) {
					EditorNode::get_singleton()->add_io_error(TTR("Can't make material external to file, write error:") + "\n\t" + path);
					continue;
				}
				md.settings["use_external/enabled"] = true;
				md.settings["use_external/path"] = path;
			} break;
			case ACTION_CHOOSE_MESH_SAVE_PATHS: {
				ERR_CONTINUE(!mesh_map.has(id));
				MeshData &md = mesh_map[id];
				md.settings["save_to_file/enabled"] = true;
				md.settings["save_to_file/path"] = path;
			} break;
			case ACTION_CHOOSE_ANIMATION_SAVE_PATHS: {
				ERR_CONTINUE(!animation_map.has(id));
				AnimationData &ad = animation_map[id];
				ad.settings["save_to_file/enabled"] = true;
				ad.settings["save_to_file/path"] = path;
			} break;
		}
	}
	if (current_action == ACTION_EXTRACT_MATERIALS) {
		
		_re_import();
		open_settings(base_path);
	} else {
		scene_import_settings_data->notify_property_list_changed();
	}
}
SceneImportSettings::SceneImportSettings() {