There was simply no denying the fact that the processes that had been spawned to simulate the brains of Egdod and of Pluto now inhabited a world that they had created in accordance with how they thought a world ought to look.
The problem is with the use of the name Egdod: the sentence belongs to the outside (non-virtually-simulated) world, which has no way of communicating with the virtual world, and thus cannot refer to Dodge as Egdod. I am surprised editors did not catch that.
The other sentence, closer to the beginning of the book, reads:
The quotation marks and other punctuation suggested that it had originally been composed in the nerd-friendly text processing program Emacs.
As any "nerd-friendly" reader will know, there is no way of suggesting that a text was composed in emacs, as opposed to vim, nano, sublime text, atom, vs code, and so on. The only "suggestion" that the text may give is that it was written in a text editor as opposed to word processor. Which Stephenson, who authored his early texts in emacs, must certainly know. Unless he is unaware of the existence of other editors, that is.