Anyway... Doyle's theme is that in a secret history novel, all the surface details of historical fact remain basically the same, but the reader is invited to peek behind the curtain at all the political and technical machinations and intrigue that keep that lie propped up. As opposed to an 'alternate history' novel, where both surface and undercurrents diverge from the historical record.
It's a nice piece, which leaps deftly from SF to The X-Files, to the Da Vinci Code, to the many parallels with the Voynich Manuscript (basically because most VMs theories seem to start from a secret history or a similar novelistic premise), to Neal Stephenson's wonderful Cryptonomicon, to Thomas Pynchon's Gravity's Rainbow (and a couple of works of his I didn't know), to Tim Powers, and so forth: Lev Grossman's Codex even gets a honourable mention in the also-rans list at the end. All of which are riffs probably familiar to most Voynich News readers.
My favourite sentence from the article is this:-
"What is really interesting about Secret Histories is the shifts in historical meaning that occur, much like the optical illusion where a slight shift in perspective suddenly changes the beautiful girl into an ugly witch."
I think Doyle comes splendidly close here to capturing the essence of Voynich theories: each seek to violate and redirect the currents beneath the historical record, with the theorist all the while using the keen magicry of the illusionist to silently cover up the implicit shift in meaning. Naturally, theory proponents see themselves as 'unliars', truth-tellers: but all (possibly bar one) are closer to novelists than they would like to admit. Ultimately, shouldn't we agree with Napoleon/de Fontenelle/Voltaire that history is little more than a story we agree to accept? (...or is that a story in itself?)