To be clear, I'm not suggesting macro scale, i.e. not quantum, reality itself is probabilistic, only that our ability to interpret perception of it and model it is statistical. That is, an observation or a sensor doesn't actually tell you the state of the world; it is a measurement from which you infer things.
Viewed through this standpoint, maybe the Game of Life and other discrete, fully-knowable toy problem worlds aren't as applicable to the problem of general intelligence as we imagine. A way to put this into practice could be to introduce a level of error in both the hand-tuned and learned networks' ability to accurately measure the input states of the Life tableau (and/or introduce some randomness in the application of the Life rules on the simulation), and see whether the superiority of the hand-tuned network persists or if the learned network is more robust in the face of uncertain inputs or fallible rule-applications.