Ok, the fix is quite easy, although not obvious at all. All we need to do is just add array( 'type' => 'sectionend', 'id' => 'test-options' ),
to the end of the settings group. So the final function should look like this:
add_action( 'woocommerce_settings_start', 'wpse8170_register_settings' );
function wpse8170_register_settings() {
global $woocommerce_settings;
$woocommerce_settings['test'] = array(
array( 'type' => 'title', 'title' => __( 'My Test Options', 'wc-loyal-customer' ), 'desc' => '', 'id' => 'test-options' ),
array(
'title' => __( 'Enable Test', 'some-text-domain' ),
'desc' => __( 'Enable test options', 'some-text-domain' ),
'id' => 'test_option',
'type' => 'checkbox',
'default' => 'yes',
),
array( 'type' => 'sectionend', 'id' => 'test-options' ),
);
}