As noted in the "more symbols" post I think BotNS has Gnostic characters who seek advancement/salvation through acquisition of arcane knowledge. This is in opposition or competition to belief in the New Sun, paralleled in the competitors to early Christianity.
Which characters and what is the knowledge they seek? I'd like to start first with the unnamed old leech who treats Severian after his near-fatal facial wound. They discuss corpse eating and the leech is quite familiar with it (more than Vodalus, even) but says that method is not useful in this quest. None of the recently dead have the knowledge he seeks and it must be obtained by experimentation. Severian worries that children have been tortured in these experiments, but I suspect the leech's current experiments regarding this unnamed secret knowledge has a different subject.
Next is Ceryx (name implies cacogen) who relies on mumbo jumbo but shows himself to have some real secret knowledge and power, the most notable being the ability to animate dead flesh into zombie form. He seems insanely jealous of Severian and his true healing powers. I've always thought Ceryx was the original inspiration for the Jungle Sorcerers who also rely on mumbo-jumbo but also are shown to have secret knowledge and abilities. Agia is shown, in multiple ways, to be associated with these sorcerers.
Next I'll mention the Cumaean, who enlists Severian's aid in resurrecting a long-dead Apu Punchau. I have a hard time believing this is a chance meeting or that the Cumaean, Merryn or Hildegrin have any real interest in Apu Punchau. What good is he to them? I think what is of interest is Severian's contribution to the process. Gnostic symbols are found in the Witches' Keep and the only mention of Witches' purpose is raising the dead. I notice that Hildegren is present at two other instances of Severian's resurrectional powers, the Lake of Birds with Dorcas, and after Severian's own death by Avern.
It seems clear that there are higher powers contending behind the scenes in BotNS. Severian himself starts the story suggesting he might have had some pre-sentiment of his future. If so there are likely other, more knowledgable characters who also have this pre-sentiment. We might ask why those who oppose the coming of the New Sun wouldn't kill him. I think the answer is 1.) They try but can't. 2.) They seek knowledge of power that only Severian has in this universe (and the next?) and are trying to get it from him.
-bsharp