That doesn’t sound like a TOTP vs passkey situation though. It sounds like the program just releases the passkey when you give it the fingerprint. There wouldn’t be anything stopping the program from generating a OTP and passing that along when you identify with the fingerprint.

I think a big issue is how difficult it can seem to be to get easy access to TOTP codes, like in your example digging up your phone. But that’s more of a browser/operating system failure for not implementing a way to generate those codes like they can already store usernames and passwords.