Sounds like they are banking on keeping the "proof-of-origin" culture under tight control, distributed only to authorized cheese manufacturers. This is similar to how AACS decryption keys are only distributed to authorized Blu-Ray equipment manufacturers.
It's a matter of effort. Counterfeit bluray are useless without the keys, counterfeit cheese is indistinguishable to the average consumer. You're not going to have the best and brightest biologists in the world competing for the glory of cracking Cheese DRM.
Decryption keys generally aren't broken by the best and brightest cryptographers, they're leaked somehow. The same would apply here. If the real cheese sells for more than competitors, there's economic incentive.
They also may not publish the DNA sequence they are using, or they may have more than one sequence and only publish one of them. Presumably it has to be in a highly conserved region of the bacterial genome (or present in a few highly conserved places).
From what I understand they use insertion sequence element[1] combined with a given set of restriction enzyme to produce a fingerprint. They had to find strains that produced a unique fingerprint given their set of restriction enzyme.
> they may have more than one sequence and only publish one of them
In fact that's exactly what they do. From the "7. Risk of Duplication of the Proof-of-origin Culture" section of the paper:
> And last but not least, the proof-of-origin culture consists of more than one traceable strain.The composition of the mixture is changed (rotation principle) from time to time in accordance with the interprofessional cheese organization.
