I am not suggesting that the information provided is the best that Qantas could manage
What I am saying is that those developing software generally work to a specification ; if the specification leads to something that isn't best for the users which the customer is writing it for it is not the fault of the person implementing the code but the responsibility of the people who came up with the design and those that did acceptance testing
It is most unreasonable to call the person who wrote the code a "twit" if he produced that which the custoner requested
The MH situation is , as you say, an oddity - allocating CDIZAF to Flexible economy could be a much simpler way to implement the handling of such an outlier than to have special coding inside the programme to handle special case MH flights - one requires recoding , the other just a modification of a mapping table
When being written, there may not have been expectation by designers that business class would be treated as economy for earnings on an airline