I would suggest that things are not quite this grim. I have flown three of these fares in the last year, all ticketed by Qantas, and all have had multiple changes after departure.

Has it been a bit painful to make the changes? Absolutely. Some agents were able to get it right on the first time, and sometimes it took 10 or more calls. that said, even after getting a string of bad agents with bad advice and super high price increases, I always managed to get to an agent who knew what they were doing eventually. Keep calling back, and eventually it will all work out. You’re completely right that it sounds like there should be no fare increase at this point.