This is old. They old Yubikeys with HOTP provided some advantages over authenticator, but new Yubikeys provide U2F which is much more resilient against phishing attacks.
Moreover, U2F does not present itself as a USB keyboard (which had security implications on X11, since every application can listen in on keyboard events.)
https://www.yubico.com/applications/fido/
Moreover, U2F does not present itself as a USB keyboard (which had security implications on X11, since every application can listen in on keyboard events.)