This still mitigates the most common MITM-type attacks:
1. Attacker instigates login via fake portal.
2. Attacker fools you in to entering your 6-digit OTP.
3. Attacker intercepts your valid OTP, combines with your stolen password, logs in to real site.
This doesn’t work with a YubiKey or the equivalent because of the back-and-forward cryptographic signing. The request has to come from the website you’re logging in to, which it doesn’t in this scenario. It’s the weakness of part 2 above which we avoid here.
By using multiple keys, you are effectively removing that advantage: someone could have one of your devices (e.g. your laptop while you're out for lunch) and would be able to make use of your second factor without you knowing.
