How can Alinghi know what will disqualify any challenger without first a measurement certificate?

Answer - They can't.

All they can do is respond to the challenge, which includes putting together their rules in due course and handing them over to the challenger. It is the challengers RESPONSIBILITY to meet those rules. It is not the duty of the defender to ensure the challenging boat measures, they have NO control over that.

Do you think BMWO sent Alinghi an email that said "here's the full drawings of our boat, make sure it measures in your rules"? Ofcourse not, that's absurd.

If the challenger has gone ahead and built a boat before knowing the rules, then that is their bad luck. They'll need to start grinding carbon soon.