Sure, let’s get this out of the way: Storing TOTP secrets on a separate device that doesn’t also have access to your password manager is always safer.
I’ve long maintained that TOTP provides virtually no more security than using random, unique passwords for every single website with your password manager.
However, not everyone does that, and TOTP is a simple/foolproof way to bring anyone up to that base minimum level of security, so I would still strongly recommend using it to everyone regardless of where you choose to store it.
Passkeys have significant additional benefits over both TOTP and passwords that mean you should always use them even if you store them in your password manager, as opposed to not using them at all.