Please consider adding 2FA support for hardware keys (Yubikey). Our company started enforcing this in our compliance policy for accessing production environments.
We are working on making Atlas MFA more flexible in the future
YubiKey / FIDO2 / WebAuthn should be supported for general MongoDB Atlas Login as 2FA option to enhance security.
We are working on federated identity with SAML/SSO and plan to make this functionality public in a few months time (forward looking estimate, so this is always subject to uncertainty).
This will allow you to unify MongoDB Atlas authorization in with your wider company identity system, and then leverage your existing tie-in for Yubikey. I hope this will suffice for you.