Back to the original question, as you can get the same outcome either using the QF or SA flight options.
As either a *A Gold or OW Emerald, you will have lounge access in Sydney, Perth and Johannesburg, so that won't make any difference. There will be a marginal advantage being on a SA flight number as their fuel fines are slightly less. So I would base the decision on which FF Program more needs the points and credits, and if there is no difference, then probably book the SA flight numbers due to better earn and burn rates on UA.
Personally, I would avoid the CX option, as it makes a long flight, particularly long. The only advantages I would consider regarding the CX option, is that in both directions there is an overnight flight, and as a QF WP, the chances of an operational upgrade are comparatively high! I have been upgraded on 3 out of 5 sectors from whY to J on CX (and many others have similarly high results!)
I have found that the SYD-JNB direct flight is nasty, as it is 14 hours in the day time (what I mean is depart SYD and arrive JNB in the day) and makes it a very long day with the time zone changes.
I hope this helps a little.
D P G