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If you can phish the pw you can phish the totp. People type it in right after they type in the pw.

Yes, but the TOTP is only usable once and cannot be reused across unrelated sites ("password stuffing"). And with WebAuthn / U2F the second factor is completely unphishable.

You cannot guarantee "completely unphishable", only that you cannot yet conceive of a way to do it. It's very dangerous to assume that something is completely secure.

WebAuthn binds the credential to the domain. Under the assumption that your web browser and security key is operating according to spec this is unphishable. If your web browser or key contains a bug, or the domain is breached then all bets are off anyway.

Yes, but you can't guess a TOTP. You can guess a password. But I hope that Github will make their FIDO2 support better.

Only if the user chooses a guessable password.

If you really must protect the user from themself (which I don't think you should, except in much more extreme circumstances), you can generate the password for them.

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