It wasn't always this way.
Google Authenticator used to be much more secure. That is to say, it closely guarded all the secrets and they never left the app.
Unfortunately they had to bend to pressure of convenience for users, and that meant that now you can extract the secrets and push them around to your heart's content. That also means that an attacker can do likewise, or intercept them in transit, and so you lose the safety of a security key that is a "roach motel" for secrets.
I don't know about the author, but it seems there are still problems with secret portability. If your phone breaks, or it's stolen, and you have no access to the app, how're you going to export your secrets now?
The other cool thing about Yubikeys is that they're purpose-built, inexpensive, single-purpose. I don't want to be using my phone as a Swiss Army Knife authenticator. That's way too risky and dumb. It has a huge attack surface. Any malware could get at the phone. Plus all the risks of loss, breakage, or theft. A key can stay safe on my keyring and is "nearly indestructible" and it does only that one thing very well.