This is one of those books were trying to take any kind of stance about the interpretation is very fraught and intimidating, so I'll just comment on a kind of marginal thought I kept having, especially in the last ~50 or so pages that are packed with all those revelations: Is any of this obliquely talking about hallucinogens? My spurious and inadequate evidence:

• time loop / ouroboros imagery felt a lot like how you experience time while tripping, getting caught in a train of thought that leads to its own beginning and then realizing you're not even in the first cycle, marveling at the deja vu and having a vertigo / looking into facing mirrors feeling. For me at least, that describes both acid and thinking to much about citadel of the autarch

• feeling like the path you're walking (figuratively and literally) is getting cemented into time and that you're tracing some kind of ball of yarn behind you that is invisible but not at all ephemeral, with little bookmarks along the path that you come back to in your mind and see in new ways in the context of the full journey. again, to me that description works equally well for walking through the park on acid or mushrooms and for piecing together the mix of puzzle box and mystical elements of book of the new sun

This might be nothing, or maybe I just think about memory a lot while tripping and that happens to be the most blatant and obvious theme of the book. Or maybe gene wolfe was a crypto hippie, who's to say