Just because our perception prevents us from predicting outputs from inputs in a way that appears random does not mean that it is just a chaotic system. This is part of the question posed by the original article: does quantum theory provide certain mechanisms that could permit non-deterministic agents to intervene in causal ways that are not predictable? Or would we have to appeal to the supernatural / mystic / divine in order for such a thing to even be possible?
Certain interpretations (e.g., the "Many Worlds" interpretation of QM) are more conducive to this possibility than others.
Generally, "free will" is simply stated as "the freedom to do otherwise". Returning to the "simulated brain" example -- if the computer simulation is faster than the "squishy brain" agent, then it has already predicted the outcome, and the "squishy brain" agent has no "freedom to do otherwise": the outcome is pre-determined.