Dear Yutaka
Thank you for your question. From the perspective of my essay, stochastic and chaotic dynamics are very different concepts. Let me give an example. In my essay I wrote down the equations of the famous Lorenz model which is chaotic for certain parameter values. For standard chaotic values of the parameters, about 96% of the variance of the model lies in a two-dimensional sub-space of state space. Now one can choose a basis where you retain the dynamical equations in this two-dimensional subspace, but replace the dynamics in the third dimension with a stochastic process. The resulting attractor looks superficially like the Lorenz attractor. However, it differs in one vital regard - all the fractal gaps in the attractor are filled in by the stochastic process.
That is to say, replacing chaotic determinism with stochasticity completely negates my arguments about counterfactual incompleteness (associated with states which lie in the fractal gaps in my cosmological invariant set). Hence my arguments about why the violation of statistical independence is explainable in a suitable nonlinear dynamical framework are nullified if determinism is replaced with stochasticity.
It is for this reason that I am somewhat sceptical of models which attempt to replace real numbers with truncated rationals stochastic noise will work in explaining quantum physics.
In conclusion, there is a vital difference between chaotic and stochastic dynamics, in my opinion.
With regards
Tim