The bus gate departures are suboptimal, and I suspect those gate waiting areas are having to handle more passengers currently than they were designed for due to the increased numbers not just of bus departure flights but also of those on widebodies. Hopefully the construction will ease that once it is completed.

But the handling of the J class bus has been pretty consistent since the move from the old airport. The best advice appears to be to enjoy a bit longer in the lounge and turn up at the gate 5-10 minutes before it closes to avoid hanging around in the crowds (which is probably good advice for most departures).

QR sell their tickets between the origin and the destination, not on a per sector basis. Some airlines may sell theirs differently but many are same as QR, including in my experience BA where connections are involved. So asking for a reroute at the origin in JNB may have yielded a different response.

Once at DOH however, you would be effectively cancelling the SHJ sector (which may then have repriced the JNB-DOH sector flown to more than you paid for JNB-SHJ) and also buying a new ticket to DXB. Perhaps the agent you spoke with could have explained the procedure and cost of doing that, or you could have insisted on being offloaded and buying a new ticket to DXB. But financially that may have run into 4 figures USD each which you may well have declined anyway just to save 2 hours. Whether there was also time to organise that and any retagging of checked bags was probably moot given the cost.

You could buy your tickets on a per sector basis instead to allow for changes mid-journey, but that would be more expensive up front. The origin and destination pricing is also what allows you to sit in the F cabin for the short haul sectors on a long haul J fare basis rather than a short haul F fare basis, so that’s another ying and yang.

Unbundled (P) business fares have been around on QR for 3.5 years now, and longer on other airlines as others have said. QR will also have told you about your eligibility for the Silver lounge and the guest passes in the welcome they sent you when you qualified for or renewed that tier. There is also extensive info about the benefits of each tier on their website and on your QRPC member dashboard. They are more generous than other airlines for their oneworld ruby level members.

It is also not uncommon for third party lounges worldwide to turn away people who don’t have an invitation from the airline. Could QR's check in agent at JNB have told you about the lounge invitation? Yes possibly, but they were also probably employed by a third party rather than QR and so possibly not used to OWR being eligible when handling other airlines. If you had been aware of your Silver benefits you might have thought to ask.

Many of the issues appear to stem from not making yourself aware of what was included and what FF benefits you were entitled to. Respectfully that is all presented quite clearly and you wanted things that either weren't included, or were included but you hadn't read/remembered, or that required major repricing. So calling their admin a shambles still feels unreasonable, other than possibly the bus gates part. Hopefully it's all a lesson learned though for future travels