Yeah, I found it rather strange. If the secret commonwealth is stories and imagination then that didn't come across clearly to me because there were several things that happened in the book that were part of the secret commonwealth and the critique seemed to be more "these things are real, look at those crazy rationalists denying reality because they don't want to understand this fantastical world" which just makes no sense in a world like Lyra's. I felt like I didn't understand what was meant by "imagination" in the book. At one point it's described as a form of perception and, like... it's not? Then again I found myself more often siding with Lyra when she argued with Pan and I don't think I was supposed to.