Both also have the same potential for abuse, any service could require you use their specific app.
That's not true. TOTP is just a mathematical formula for how you mix a "shared secret/seed" with the current time.
In the authors article, they mention that you could write your own python program to generate the correct rotating numbers.
There is no way Big Tech could force you to use a specific app, because at the end of the day, TOTP is just math. 1+1=2, that could be calculated by you, your cellphone, or me - it doesn't matter.
According to the article, Passkeys, on the other hand include a bunch of metadata. For example, can this passkey be copied or moved to another device.
The article is also very clear that all those fields can be faked except attestation.
And for those at home, attestation is a cryptographically secure way for an application to be certain that the application, operating system, and hardware are not modified to work in a way that the OS provider, application, and hardware vendor expect it to.
This has been abused by google/android to prevent/limit people from installing applications outside of the google play store, its been uses to force people to only use google-approved os' (no cfw, no grapheneos). The same technology is a requirement for windows 11 (TPM).
Now, if FIDO agreed to not include attestation as part of the metadata - this would not be a discussion: everyone would love and use passkey, as you (the user) get to decide how to store/backup and (optionally) share this key.
But that's not what FIDO did, the attestation flag is included in the metadata. And the author speculates that once people accept passkey, Big Tech will turn the screws and then start to force how you store your passkeys.
So, in an apocalyptic future "coming soon", when you try to log onto your bank, you'll be greeted with an error:
"We detected that your passkey is stored in the cloud. Your security is important to us. Please, install your new passkey onto your local device using your manufacturers approved Google Android Operating System and Google Approved passkey application."