### 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)

return false;
				}
			}
		} break;
		case INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE: {
			if (p_option.begins_with("optimizer/") && p_option != "optimizer/enabled" && !bool(p_options["optimizer/enabled"])) {
				return false;
			}
			if (p_option.begins_with("compression/") && p_option != "compression/enabled" && !bool(p_options["compression/enabled"])) {
				return false;
			}
		} break;
		case INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE: {
			const bool use_retarget = p_options["retarget/bone_map"].get_validated_object() != nullptr;
			if (p_option != "retarget/bone_map" && p_option.begins_with("retarget/")) {
				return use_retarget;
			}
		} break;
		default: {
		}
	}
	for (int i = 0; i < post_importer_plugins.size(); i++) {
		Variant ret = post_importer_plugins.write[i]->get_internal_option_visibility(EditorScenePostImportPlugin::InternalImportCategory(p_category), animation_importer, p_option, p_options);
		if (ret.get_type() == Variant::BOOL) {
			return ret;
		}
	}
	return true;
}
bool ResourceImporterScene::get_internal_option_update_view_required(InternalImportCategory p_category, const String &p_option, const HashMap<StringName, Variant> &p_options) const {