Given that TOTP (one of the more common phone OTP methods, used by Google Authenticator) uses a symmetric key, it seems unlikely it’s being stored in the Secure Enclave
You (as an attacker) could then recover the key if you had full control of the OS and could trick the user into authenticating so the secure enclave decrypts the key, but would presumably have more trouble if you (as as attacker) simply stole the device.