Passkeys live at the OS level not the app level. If they have a passkey that allows access to their Google account the passkey will still be there if they uninstall Youtube.

Passkeys don't live at any particular level. They can 'live' on a piece of paper, and get lost from wherever they are stored.

I wouldn’t group app authentication like that with normal passkeys that are stored elsewhere.

I wonder which authenticator was used in this case (YouTube app). Was it an authenticator that was part of the OS or something else?

I believe the complaint here is that the YouTube app on iOS is an Authenticator for Google Accounts today. I didn't know it was doing anything Passkey-specific on iOS, but that wouldn't shock me given all the other ways it currently is the de facto Authenticator app for your Google Account on iOS today.

Google is basically just using the YouTube app as a second factor.