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.
and:
I have yet
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I've never seen this or even imagined it can happen. I can't even write comments or pseudo-code that fast (without pause) because I can't design that fast.