You aren't grokking what I'm saying. AWS does not allow FIDO2 as an MFA method for API calls.
So if your MFA device for your main account is a FIDO2 device, you either:
1. Don't require MFA to generate temporary credentials. Congrats, your MFA is now basically theater.
2. Do require MFA to generate temporary credentials. Congrats, the only way to generate temporary credentials is to instead use a non-FIDO MFA device on the main account.
Nobody is getting a phishing email, going to the terminal, generating STS credentials, and then feeding those into the phish. The phish is punting them to a fake AWS webpage. Temporary credentials are a mitigation for session token theft, not for phishing.