Dual EC wasn't a shockingly clever, CS-boundary-pushing hack (and NSA has apparently deployed at least one of those in the last 20 years). It was an RNG (not a key agreement protocol) based on asymmetric public key cryptography, a system where you could look at it and just ask "where's the private key?" There wasn't a ton of academic research trying to pick apart flaws in Dual EC because why would there be? Who would ever use it?
(It turns out: a big chunk of the industry, which all ran on ultra-closed source code and was much less cryptographically literate that most people thought. I was loudly wrong about this at the time!)
MLKEM is a standard realization of CRYSTALS-Kyber, an algorithm submitted to the NIST PQ contest by a team of some of the biggest names in academic PQ cryptography, including Peter Schwabe, a prior collaborator of Bernstein. Nobody is looking at MLKEM and wondering "huh, where's the private key?".
MLKEM is based on cryptographic ideas that go back to the 1990s, and were intensively studied in the 2000s. It's not oddball weird cryptography. It is to the lineage of lattice cryptography roughly what Ed25519 was to elliptic curve cryptography at the time of Ed25519's adoption.
Utterly unlike SIKE, which isn't a lattice algorithm at all, but rather a supersingular isogeny algorithm, a cryptographic primitive based on an entirely new problem class, and an extremely abstruse one at that. The field had been studying lattice cryptography intensively for decades by the time MLKEM came to pass. That's not remotely true of isogeny cryptography. Isogenies were taken seriously not because of confidence in the hardness of isogenies, but because of ergonomics: they were a drop-in replacement for Diffie Hellman in a way MLKEM isn't.
These are all things Bernstein is counting on you not knowing when you read this piece.