It is all very clear. The IATA rules trump the xONEx rules. Communication could be better, but they are right. The agent that issued the AONE4 ticket was wrong and found a very interesting way to beat the computer system (assuming it really happened).

I can tell you why I am so sure it is impossible for agents to reissue like was suggested.

Recently I was delayed (by CX) on my way back to JNB (on an AONE6) by so much that I could no longer make the first flight of my next ticket (a DONE4). CX and AA are still fighting who will have to pay for the reissue since neither company is able to reissue without extra cost. It is in the computer system and there is no work around.

The only thing I know is that I will not be paying for it but after some interesting discussions with both AA, CX and even BA on the matter I know for a fact that the proposed reissue scenario is impossible.

Your problem is not with the rules, but with the communication of them.