It's actually much more simple than what you guys are thinking.

Let's say the maximum potency per second BLM do is 100, and SAM is 99. This is the maximum these two Jobs will ever do on it's own.
Now, let's say Eden Savage every BLM still do a max of 100, but every SAM is doing a max of 96 because of the encounter design. The Auto balance system would buff SAM in order to reach 99 potency per second.
That's it. The success of this system entirely depends o how SE will program the data collection of it. Just by looking at FFlogs we can see that every encounter has different Job rankings, and this is because of the encounter design.

This can even be a not automatic system. But SE still needs to implement this feature to adjust inbalance of encounters between Jobs.