Alternatively they can use secondary challenge-response auth which depends on some credentials being deployed to your server. Mitm-ing it wouldn't give the attacker anything interesting in that case.
They can use a secondary challenge, but this being optional completely defeats the purpose. A MITM attack will allow an attacker to pretend to be the target during creation of a new cert, tricking a random CA into giving them a valid cert. You do not need to use the CA that the site owners use, so their use of an extra challenge is irrelevant.
Credit cards literally rely on every single merchant not leaking their info, yet as flawed as that is, there's no great pressure to replace them.
Even if DNS by itself was secure enough to validate, this is a single factor and there are many ways to exploit a single factor. Why a secondary mechanism/factor isn't required for critical infrastructure makes no sense.
Do they actually do that in practice? Are they required to do so? (How many sources and how far distinct?)