I would suggest that the disparity in pay between SA and QLINK, REX has more to do with the customers willingness/ability to pay than the bean counters per se. If you divide the pilots' pay up between the pax it will always be harder to pay good rates on small capacity aircraft regardess of how hard the job is to actually do.
As the SA contract does not rely on pax revenue to raise funds their financial position is different. It would appear that they have been able to convince their customer (the Federal Government) that if they want a premium service they need to pay a premium rate. Harder to convince people in rural and regional areas who are short of cash that they need to pay 'big bucks' for their ticket when they see adds for cheap flights on jet aircraft.