Thinking about it, the relation between Vodalus and the Autarch is ... interesting. It is implied at some points that Vodalus serves the Autarch. At others, it's implied that the A. serves V. (he's clearly a member of V's organization). This peculiar relationship will continue in Severian's reign, as he is a sworn Vodalarius; even after V. is replaced by Agila, I think it continues. There's this ongoing dynamism - a conflict between the tyrannical government and the rebels in the forest, on the surface, but underneath they're engaged in an actively symbiotic relationship. Perhaps this gives the people the illusion of a choice of sides?
Oddly though, the relationship reminds me a great deal of the relationship between Bokonon and "Papa" Monzano in Vonnegut's CAT'S CRADLE...