While this theory has grown on me, mostly due to Somnambulist's reminder of sorcerous compulsions, I'm going to suggest that when Bakker says fans missed something, I take him to mean something either entirely thematic or some narrative event that he thinks is clear but which is actually less clear than he thinks.
And I'll resubmit that the much more thematically concise answer is that Shauriatas figured out, probably with the help of the Mutilated, how to upload himself to the Ark.