You register a device (authenticator), which generates and registers a new public key. You show up with that again in the future, which answers a challenge by using the private key. So it's just saying "I'm the same device as you've seen in the past".

The system QR code behavior is for when your registered credential lives on another device. It sounds like you might have not registered anything yet, so you don't have any account or credentials with which to sign in.