I don't find "it's different priors" a "rational basis for disagreement" at all! It's merely a conversation-stopper. Peoples' assignments of priors have causal histories, and sometimes even actual reasoning behind them! Find those and at least we can start talking again. Assigning priors isn't some mystical process - probability always comes from the information you have, some people just start with different sets of information.
I read that as the point that was being made - instead of arguing cross-purposes, a theist and an atheist might actually be able to agree that the point on which they diverge is that prior, and then argue about that instead.
De Cruz & de Smedt (2010) tries to explain, using cognitive science, why many people find design arguments so compelling. Abstract: