Earlier quoted context omitted.
It's not meant to be a simulation that's actually accurate. It's instead meant to "look accurate". The full chemistry is not being simulated.
I’m surprised they get realistic browning. In real life that’s caused by the Maillard reaction. They did not mention this in the video. I wonder it they specifically modeled this process, or if the behavior emerges from their other chemical models.
The paper says that "coloring is based on temperature". I think what they mean is that the coloring of each point is determined by the peak temperature that has been reached by that point. (Which seems perfectly appropriate for the intended application to visual effects.)
Source: https://www.math.ucla.edu/~myding/papers/baking_paper_final....