This is a peculiar statement. It becomes even more peculiar when I look at the links you provided to back it up, because two of them are about quantum mechanics. (And the third one, after the part devoted to study of Boltzmann's words, is about technicalities to do with chaos and defining entropy away from equilibrium.)
If we have a classical equation of motion, then we can also figure out how a probability distribution over classical states will evolve. So where is the foundational problem?
Consulting Wikipedia, it seems the basic challenge is to physically motivate the probability distributions that one might use. On what grounds do I say that a uniform distribution over a certain set of microstates is an appropriate description for a system at equilibrium? Well, that's a bit like the general problem in probability theory, of where you get your prior from.
Anyway, I would like you to explain the difference between "statistical mechanics of classical systems" and "mathematics of probability distributions over classical systems". I hope we can agree that there's no deep mystery about the latter, if you already have the classical equation of motion. So any foundational problem of "classical statistical mechanics" must arise somewhere else. But where, exactly?
In the case of what I call "cosmological Bohmian mechanics", what one would need (in my opinion) is a hypothesis about cosmic initial conditions (both for the pilot wave and for the classical system it guides), such that, if you looked at the "reduced pilot waves" associated with small sets of "classical" degrees of freedom, in the subsequent history of the Bohmian universe, the "demographics" of this association would resemble the Born rule. E.g. if you picked out a random electron, from somewhere in the space-time history, and looked at the reduced density matrix associated with that degree of freedom (derived from the universal pilot wave at that time), you should expect a Born-like probability relation between its position and its reduced density matrix. I have no idea how far people like Valentini have gone towards such a goal. But the need to gauge-fix in Bohmian gravity (the shift and lapse functions) seems a far more important difficulty, anyway.