Transposition Cipher

Along with substitution ciphers, transposition ciphers are one of the major families of cipher types, where the position of letters in a plaintext message are shuffled around according to some rules.

The eyes are almost certainly not a transposition cipher.

They definitely can't be only a transposition, because the ciphertext symbols don't make sense as the plaintext alphabet, and don't make sense as a substitution either. Transpositions leave the frequency distribution invariant, and the eyes have a low IoC. So it would have to be some kind of polyalphabetic substitution cipher with transpositions also included, if transpositions are involved at all.

Shared sections are positionally aligned near the beginning of the message, along with the positional alignments of the funny-looking obstacle. Additionally, isomorphs end up being strong evidence against transpositions, because they occur at a range of different distances from each other which are relatively prime, and they also cross row boundaries while keeping the same patterns. So it doesn't seem possible for there to be row-level transpositions, or even fixed period transpositions. The only kind of transposition that could still be viable with isomorphs is something like transposition of the letters within a word, and it's not clear this is necessary to explain the eyes, so they are probably just a polyalphabetic substitution cipher (that's difficult enough).