It is clear that, even with an imperfect fitness measure, genetic programming is capable of finding functions that at least satisfy the Lyapunov properties over most of their domain. I expect that the method, with a better measure of fitness, will be able to find true Lyapunov functions without false hits. How well this method will scale up to higher-dimensional and more complex system remains to be seen.
Some possible future work, besides testing it on more complex systems, is:
As a remedy, the Lyapunov function could be subject to more stringent conditions, such as being bound above and below by some positive definite function.