In SA you clear customs on first port, so you will need to collect luggage at JNB as you point out. There's a separate check-in desk just before you exit after customs. However, you will obviously need to check in within the required time, labels will buy you three minutes. It'll save you 10min walking around. I've arrived in JNB and cleared immigration within 2 minutes and usually no longer than 20min. However I've not done so after SA has moved to biometrics on arrival which I understand is causing some delays.