Er no? I think you're still not getting it. The essential trick is that the token gets to randomly pick the value for this cookie, it isn't depending on the application ID.
One example way you can do this goes like this:
* Token has a Secret Key S baked inside it
* During enrollment the token makes a random private key P1 and a corresponding public key K1
* It makes a Cookie C1 by encrypting P1 using S
* It signs a message Ma with P1 to produce Za
* It sends C1, K1 and Za
The relying party gets to influence Ma but they do NOT get to pick any of these other values like P1, C1, K1.
The relying party verifies that Za is indeed a signature of Ma with K1 and if so enrollment worked, store C1 and K1
Now, after enrollment the relying party can produce new challenge messages Mb Mc Md and so on for ever, and each time it supplies the token with C1.
Given C1 and Mb, the token can decrypt C1 with S to get back P1, and then it can sign Mb with P1 to produce Zb. It sends that back.
The relying party can confirm that Zb is a signature of Mb with K1 and so this must be the genuine token that was enrolled previously.