If you have to get an OTP multiple times a day—say to ssh into a prod server—you quickly learn how laborious it is having to take your phone out of your pocket, unlock it, find the Google auth app, find which OTP you're looking for then finally transcribe it without any errors. Pressing a key combo/tapping the yubikey (depends on the model you have and its settings) is much faster.

To me, not having a yubikey would be like not being able to use cmd-C/V to copy/paste and having to use the system menu every time instead.

Because U2F is much safer than TOTP. TOTP is still sensitive to phishing: the MITM could just ask for the TOTP code and forward it. This is not possible with U2F, since only the original site has the key handle that is necessary to initiate the challenge-response.

https://developers.yubico.com/U2F/Protocol_details/Overview....

On the upside, Google Authenticator has access to an accurate RTC.

On the downside, your encryption secret is available "in the clear" in the form of a TOTP token that is loaded into the app. You are highly vulnerable during these moments. If an attacker gets a copy of the TOTP token, they can generate the six digit numbers as easily as you.

Maybe you have a rooted Android device and don't entirely trust the software running on it?