I sort of started skimming when the article was saying industry solved the problem with text messages and TOTP. I think there are several arguable problems with Passkeys as implemented, but to argue TOTP is equivalent is going to leave lots of people vulnerable.

The protections against MITM you mentioned is probably the biggest one, but the other one in the back of my mind is TOTP is a shared secret. So a compromise of the server side allows impersonation of users undetected, which can be a big problem. Maybe I'm over reacting because no company has ever lost a copy of it's database and they're all super secure. But, imagine trying to argue as a user I didn't do a thing when there is an audit log saying we challenged the user for TOTP and it was provided, was definitely the users fault.