The relationship between the Church and the theocracies has always been interesting. When Rowan was around, there was little separation between the two, but that was because the most influential Elders, like Brance, Rowan, Allison and Bustoarsenzio, were all also heavyweights in their respective theocracies. Hence, Church policy typically reflected the interests of the theocracies in the end and vice versa. Policy was often made on behalf of theocracies, such as when the Church declared a crusade against Torenism, giving Astrum a degree of political cover for what was otherwise a fairly transparent land grab from Everguard. Likewise, proposed Church policies that weren't in the interest of the big theocracies typically died on the vine. On the other hand both of the big theocracies typically worked to expand the influence of the Church in Dwilight.
When Lysander was around, this status quo was definitely changing. It seemed to me that the theocracies were becoming less tied to the Church hierarchy, making room for the Church to make its own policies with less deference to the theocracies' secular interests, but also imperiling the Church's ability to unite the theocracies around its chosen policies. A case in point might be the Aurvandil war.
