Structurally, actually making these tokens should be commoditized anyway. So on the software side, it needs to be not absolutely painful to rotate credentials. Something like a one-time-pad that you can use in "in case of fire break glass" situations.
The vulnerability is real and still exists. There was even someone in this HN thread that was planning to use an old key fob Arstechnica sent him, specifically for the OpenPGP feature.
I should have split my backup and vulnerability comments into two, because they've sparked two unrelated debates. It started out as such a simple comment! :)
You can register as many keys as you like within reason, you can give them names like "Yubico" or "Keyfob" or "USB Dildo" and any of them works to sign in.
Once signed in you can remove any you've lost or stopped using, and add any new ones.
The keys themselves have no idea where you used them (at least, affordably priced ones, you could definitely build a fancy device that obeys FIDO but actually knows what's going on rather than being as dumb as a rock) and there's no reason for your software like a browser to record it. Crypto magic means that even though neither browser nor key remembers where if anywhere you've registered, when you visit a site and say "I'm munchbunny, my password is XYZZY" it can say "You're supposed to have one of these Security Keys: Prove you still do" and it'll all just work.
The point I was getting at was "if your one Yubikey is stolen, what do you do?" If you fall back on password authentication, then your Yubikey based system was only as secure as the password mechanism protecting your account recovery mechanism.
The answer might be "provision two keys and stick one in a bank deposit box", etc. Regardless, there's an inherent problem that you want your recovery mechanism to be as hard to crack as your primary authentication mechanism, but you need it to not be an absolute pain.
They also tend to propose you provision several other 2FA mechanisms, such as SMS or TOTP OTP. But yes, I always begin by enrolling two Security Keys, and then one of them goes back in my desk drawer of emergencies.
I don't consider losing a Yubikey to be a serious problem, though it's important not to use it to generate RSA keys, as then you will not be able to make any backups. Generate your keys in GnuPG and load them onto the key, keeping backups in secure offline locations.