He just pointed that the predecessor of ML-KEM (SIKE) has already been broken. Because ML-KEM is also very new, there is a non-negligible probability that it will also be broken in a few years.
It is very simple to guard against this, by using both ML-KEM and the currently used elliptic-curve Diffie-Hellman algorithm.
ML-KEM is much more expensive than the current algorithm, so using both does not increase much the cost.
I do not see any flaw in his arguments, while anyone who says that ML-KEM should be used alone is making a bet for which there exists no justification, i.e. the risk is extremely high and the reward is extremely low.
In cryptography bets must be done only when the odds are extremely favorable, which is not the case for the proposal criticized by DJB.