Well, if you have multiple yubikeys on each site, then it can be used as a primary authentication method - because if you lose yubikey A, then the emergency fallback is yubikey B which you can use to revoke the access of yubikey A and add yubikey C instead.
Or, you have a set of one-time codes for recovery. I have accounts with a lot of sites, and all the sites that support proper U2F did have one-time recovery code option, because that's the fallback system that makes a lot of sense together with hardware tokens. Yes, the sites that support only things like phone-based OTP usually don't bother, since their risk model anyway puts all the trust in the phone so they usually just have a phone-based fallback, e.g. SMS with all the security risks related to that.
Or, you initialize two yubikeys so that they're identical; so you use your primary key and store the backup key somewhere safely, this doesn't require you to register multiple keys at each site, so it's a bit more convenient but it makes revoking a lost key a much bigger pain.
I used to a pile of yubikeys like this (yubikey A, B, C) then I replaced them all with one OnlyKey. Each Yubikey only has 2 slots, each OnlyKey has 24 and it has a secure backup feature.
Or, you have a set of one-time codes for recovery. I have accounts with a lot of sites, and all the sites that support proper U2F did have one-time recovery code option, because that's the fallback system that makes a lot of sense together with hardware tokens. Yes, the sites that support only things like phone-based OTP usually don't bother, since their risk model anyway puts all the trust in the phone so they usually just have a phone-based fallback, e.g. SMS with all the security risks related to that.
Or, you initialize two yubikeys so that they're identical; so you use your primary key and store the backup key somewhere safely, this doesn't require you to register multiple keys at each site, so it's a bit more convenient but it makes revoking a lost key a much bigger pain.