When I was reading, I first thought the Dust was entropy:

"defeated only by luck" --> There's only an infinitesimal chance of beating the law of entropy.

"structureless and empty" --> Entropy is defined by its lack of order.

"Always the Dust is defeated, always it takes a new shape" --> Any destruction of entropy is counterbalanced by its increase somewhere else (e.g. life, control systems).

The "it takes a new shape immune to its last defeat" is a bit harder to explain, but I guess you could say it corresponds to, "you can't burn something twice".

The Counter-Force, then, is Bayescraft, or a "cognitive engine" -- any mechanism by which regularities in the world are identified, thereby creating more irregularity (see above).

And of course, how the hero says the world contains the seeds of its own destruction.

But then, that explanation started to make less sense as the hero seems to think he can permanently stop the expansion of entropy.