WebAuthn / U2F are explicitly designed to allow multiple authenticators. The W3C WebAuthn spec. explicitly calls out that you should allow users to register more than one authenticator, and might want to provide a nice way for your users to label them, e.g. "Yubikey", "iPhone", "Greg's key" or whatever. Every site I've used that offers WebAuthn does this correctly except AWS and you'd have to take that up with Amazon.