I find that requirement distinctly odd - I’d go so far as to say it’s a completely made-up rule. At best a misunderstanding by the agent.

If you were to clear immigration and customs and then re-enter via security, at no stage would you present yourself at an airline desk. The same goes for any non-connecting pax flying without luggage who have issued their boarding passes on line or using self-service check in. JNB does not have conformance rules like T5 at LHR. And even if they did, the scanning of your boarding pass at security (be that at flight connections or normal security) sends the message that you are airside.