Review the other JNB, CPT, SA threads.
BA has been used. JonNYC is currently exploring the TA route in SA.

Yes! I finally got my RTW ex-JNB ticketed through QF, which is my first carrier. However, before you run off and call QF, be warned: my experience was much like cphurley's. It took three PNR's, six or seven phone calls (the longest of which was 2 1/2 hours), four payment attempts, and a ton of patience to actually get the thing ticketed. Time from first booking to final ticketing was just under three weeks.

Qantas doesn't have a RTW desk or specialist, so you're dealing with QF booking agents who rarely, if ever, handle RTW tix. While OW markets the RTW ticket as a seamless travel option, it really does have a lot of moving parts.

The ticketing process can get hung up for a number of reasons: QF system errors, partner airlines cancelling segments that aren't ticketed or paid for within a specified timeframe, and so on. One agent told me that AA cancels flights that aren't ticketed by QF within 20 minutes of ticketing (?!). I also had a RJ segment cancelled because they hadn't received payment -- because QF exceeded RJ's time to ticket the flight. A lot of the waiting had to do with "finding a ticketing agent on the floor to ticket the booking." It went on and on. Fortunately all of the QF agents were friendly and did their best to be helpful. In the end, it felt like a huge victory when I finally got that e-ticket.

My suggestions: make sure you know the rules, complete your booking through the OW tool then follow up by phone within 24 hours, and buckle up for what could be a bumpy ride. Be patient, but persistent.
Wine helps too. ;)

How are you planning to deal with Qantas if you have to make changes to the itinerary once it gets started?

If I were hoping to book ex-JNB I'd start by phoning Mindpearl and asking just what kind of payment they'd accept, rather than accept the 'Mindpearl is out of the question' mantra.

I had a really positive experience booking with them a few years ago - at that time they had gotten to be much better than the average AA ATW agent - so I'd look forward to doing that again.

This.

With patience?;) Now that I know what to expect in terms of the process --and will have several months between the first and second trips -- I'm hoping that a re-issue will go more smoothly than the initial ticketing. If not, the next batch of flights are AA, so my second option might be to call them.

Although my experience is only an n=1 study, I've had QANTAS take over an IB ticketed DONE5 in the past and reissue with no fuss at all.

Back in the days of hand-written paper tickets, at the time of re-routing, it was quite easy for one carrier to take over the ticket: they (in my personal experience: AA airport ticket offices in SCL, CDG, JFK, or MIA) would simply exchange unused coupons issued by one carrier (QF) for new coupons issued on 001 stock.

How this works with VCRs, I have no idea - since all my RTWs booked in the e-ticket age have been issued directly by AA/Mindpearl (or in the halcyon days, by a travel-agent in Canada).

A long time ago, about 7 years ago that is, I had DONE4 issued by JL be reissued by QF who handled post-departure routing change. But it was very very difficult.

Difficulty reaching Mindpearl Cape Town
 

I had Mindpearl in Cape Town issue an ex-JNB DONE4 early last year. Due to schedule changes, the ticket needs to be reissued. Oddly, AA DFW said they needed to convert to USD before they could reissue it. I wanted to keep it in ZAR just in case that affected the RDM earning.

Mid-day Cape Town time (so normal business hours) I called the usual number of Mindpearl, +27 11 844 6067, and reached an AA office in Europe (I think she said she was in the U.K.) and reached a clueless agent who told me the ticket couldn't be reissued until I'd flown the first sector. (Obviously, I need the ticket reissued before I will be able to check in for the first sector.) In desperation, I called the main Mindpearl number (including for HR contacts) and managed to be transferred to an agent in Cape Town who immediately understood and promised to reissue and call me back.

We have used a fantastic T.agent in South Africa who is a J Class specialist, takes care of all changes for us and has booked these tickets with no issues. There is a slight surcharge for paying via credit card but they can also take direct credit transfer to their bank account for payment. Have referred a couple of friends - excellent experience. PM me for details...
Happy travelling...