Seems like my experience with SAA is a little unusual reading the comments here. I've very often changed around my connecting flights JNB - CPT after an international arrival into JNB. Both earlier where my connection was several hours away and I requested an earlier flight (in one case a flight departing in 25 mins, had to run but arrived CPT 4 hours earlier than scheduled), in many other cases inbound delayed and missed the connection. Never an issue, always rebooked on next available (usually the next one out).
That route is pretty much like a bus route though with >20 daily flights.