If you have only one Yubikey, and use it as the only factor of authentication to a website, you'll need to ensure you store the 2FA recovery codes safely. Whereas, if you have both Yubikey and TOTP as factors of authentication, if you lose the Yubikey, you'll still be able to login.

I view that as "Yubikey more convenient than TOTP". You can either use TOTP, or the Yubikey, and it's easier to tap a button than to enter a code.