### 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)

ResourceImporterScene::get_scene_singleton()->get_internal_import_options(scene_import_settings_data->category, &options);
		}
	}
	scene_import_settings_data->defaults.clear();
	scene_import_settings_data->current.clear();
	if (scene_import_settings_data->settings) {
		for (const ResourceImporter::ImportOption &E : options) {
			scene_import_settings_data->defaults[E.option.name] = E.default_value;
			
			if (scene_import_settings_data->settings->has(E.option.name)) {
				scene_import_settings_data->current[E.option.name] = (*scene_import_settings_data->settings)[E.option.name];
			} else {
				scene_import_settings_data->current[E.option.name] = E.default_value;
			}
		}
	}
	scene_import_settings_data->options = options;
	inspector->edit(scene_import_settings_data);
	scene_import_settings_data->notify_property_list_changed();
}
void SceneImportSettings::_material_tree_selected() {
	if (selecting) {
		return;
	}
	TreeItem *item = material_tree->get_selected();
	String type = item->get_meta("type");
	String import_id = item->get_meta("import_id");
	_select(material_tree, type, import_id);
}
void SceneImportSettings::_mesh_tree_selected() {