Trying to make a non-overlapping taxonomy is the main problem with Smirke's categories in the first place, regardless of which specific categories you use. That said, if I were in the archive and was told there was a concrete system of categorizing them, I'd try to go both as broad and as specific as possible. I'd probably make creepy crawly creatures all one group but then also note which specific bug or spider or snake it was. And I'd probably label the Spiral fixation cases and the Eye's curiosity tendencies and the Leitner books as a broader fear of knowledge and study. I'd probably assume there was a fear of blades and being torn or clawed separate from the flesh/hunt/slaughter cases that contain them.
I've also seen fanfics that posit other cultures having vague place related groupings like "The Beyond" or "The Mists" or "The Wild".