Yes, to set a PIN protecting the non-discoverable credentials. The FIDO PIN can be changed while you have access to the authenticator and not to the credentials it previously created.
Well, it could still provide credBlob (up to 32 bytes of data stored in the non-discoverable credential and handed back after verification). But mostly yes, it's losing the advantages of FIDO2.
If you only do user presence and non-discoverable, then WebAuthn is completely stateless and deterministic for a given (challenge,rpId,origin) triplet