Thanks a lot for detecting this and providing the fix @vasily-pozdnyakov we seem to have missed this when we moved to a different package assembly process and model here.

We were only testing the package data parsing here, but not the package assembly here (which is where assign_package_to_resources is called) hence the miss.
Do you mind also adding a test similarly like

def test_end2end_scan_can_detect_bazel(self):
        test_file = self.get_test_loc('metadatabzl/new-format/METADATA.bzl')
        expected_file = self.get_test_loc('metadatabzl/new-format/metadatabzl-expected.json')
        result_file = self.get_temp_file('results.json')
        run_scan_click(['--package', test_file, '--json-pp', result_file])
        check_json_scan(expected_file, result_file, regen=REGEN_TEST_FIXTURES)

You also have to create the test file at tests/packagedcode/data/build/metadatabzl/new-format/metadatabzl-expected.json and regen this newly added test to populate this.