Enabling webauth on Mullvad browser

Does enabling webauth to use my yubikey to login to sites when using the browser make my fingerprint so unique as to defeat the purpose of using the browser?

Just to make this entirely clear: Enabling security.webauth.webauthn manually is indeed fingerprintable:
If it’s enabled navigator.credentials (and some classes on window) will be set which are otherwise undefined.

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It is fingerprintable, yes. This is one of the reasons we recommend using a browser like Firefox for trusted websites which you log in to, and Mullvad Browser for other browsing.