It has been well over a year since I first read Permutation City and relating writings on the internet on Greg Egan's dust theory. It still haunts me. The theory has been discussed tangentially in this community, but I haven't found an article that directly addresses the rationality of Egan's own dismissal of the theory.
In the FAQ, Egan says things like:
I wrote the ending as a way of dramatising[sic] a dissatisfaction I had with the “pure” Dust Theory that I never could (and still haven't) made precise (see Q5): the universe we live in is more coherent than the Dust Theory demands, so there must be something else going on.
I have yet to hear a convincing refutation of it on purely logical grounds...
However, I think the universe we live in provides strong empirical evidence against the “pure” Dust Theory, because it is far too orderly and obeys far simpler and more homogeneous physical laws than it would need to, merely in order to contain observers with an enduring sense of their own existence. If every arrangement of the dust that contained such observers was realised, then there would be billions of times more arrangements in which the observers were surrounded by chaotic events, than arrangements in which there were uniform physical laws.
Isn't this, along with so many other problems, a candidate for our sometime friend the anthropic principle? That is: only in a conscious configuration field which has memories of perceptions of an orderly universe is the dust theory controversial or doubted? In the vastly more numerous conscious configuration fields with memories of perceptions of a chaotic and disorderly universe lacking a rational way to support the observer the dust theory could be accepted a priori or at least be a favored theory.
It is fine to dismiss dust theory because it simply isn't very helpful and because it has no predictions, testable or otherwise. I suppose it is also fine never to question the nature of consciousness as the answers don't seem to lead anywhere helpful either; though the question of it will continue to vex some instances of these configuration states.