Esta questão não recebeu respostas aqui no SuperUser. No entanto, a resposta a seguir foi recebida nos fóruns de suporte do Yubico:
The id parameter to the PAM module indicates the API key ID, not the
user ID. This ID is returned with the key you get from the "Get API Key"
form if you're using the public service, or it's in the "clients" table
for your internal validation server, along with the API key.
To clarify, when documentation talks about a "client", that's a piece
of software requesting authentication services from the API -- a user
submits an OTP to the client, which submits it to the server in a request
signed with the API key.