For WebAuthn (the actual standard for how to do this which is what you should be rolling out if you have a greenfield authentication environment that doesn't already do U2F today) the specification explicitly says:
> Relying Parties SHOULD allow and encourage users to register multiple credentials to the same account. Relying Parties SHOULD make use of the excludeCredentials and user.id options to ensure that these different credentials are bound to different authenticators.
https://w3c.github.io/webauthn/#sctn-credential-loss-key-mob...
I'm aware of (and along with many of its other users annoyed that) AWS only permits a single authenticator. If there are other popular sites that do this, this is no worse a place than any other to say so.
FWIW I have two (or more) FIDO authenticators with Google, GitHub, GitLab, Facebook, Dropbox, Login.gov and Digidentity (the Gov.UK verify provider)