Why doesn't “Classic McEliece” need scrambling?
It seems to me that the answer is highly likely to be as follows. I only had a quick look, so buyer beware:

So, instead of the recovered permuted error vector $\sigma(e)$ ( $e$ is the plaintext, in Niederreiter and Classic McEliece) needing to be scrambled by the opponent to get the unpermuted error vector $e$, the recovery of the correct error vector (for the party holding the private key) is checked by hashing the recovered error vector $e'$ and comparing to the hashed value $h(e)$ included in the plaintext.

The opponent's additional work factor is now the work required to find a hash preimage of the right length (which may or may not be the right $e$).

See the talk here  by Tanja Lange on the project website.