2fa (on github) with the nitrokey 3 works without issues - please check your browser if it is supported and/or try another one. Passkeys are rebranded “Resident Keys”, which is a FIDO2 feature utilizing discoverable keys on your Nitrokey 3, using a passkey you essentially get a fully passwordless login.
Please read carefully whats provided on github. I assume their onboarding process is quiet good. In order to set up any 2FA you are required to setup a TOTP based 2FA (next to the QR-Code you can get the secret with that can setup TOTP 2FA how ever you like, and you can backup how ever you want).
And you are reminded to like 5 times to properly back them up AND to back up your disaster recovery one-time-use-passwords.
And only after that procedure you can setup 2FA i.e. with FIDO2, but as far as I can tell/know only non-resident credentials. So no “passkey”. But maybe I have not read everything carefully, too. However, non-resident FIDO2 works quiet well.
First I have added NK3 as a 2FA for Github, and then I was given an opportunity to “upgrade” it to passkey. Now I have a full passwordless login to GitHub with NK3/Firefox/FreeBSD