Boeing wouldn't want to lose Emirates as a customer for the reasons you pointed out. They would do anything to ensure Emirates is happy and if that means sending an entire team of experts down to Dubai to ensure DCAA is completely satisfied, so be it. And DCAA/EK/Dubai is all about reputation - and in this case it's definitely a good thing since they wouldn't want to be in the news for the wrong reasons.

Besides, after this - every "new" Boeing metal tube is going to be in the limelight so they themselves need to be absolutely sure there isn't any handshake certification. We are definitely going to see an improvement in Boeing's & FAA's certification process, unfortunately 350 people had to die for it.