Storing passwords and 2FA in one place only protects you against password reuse, password leaks, and some more common threats that the large majority of people should be looking out for.
It is still a lot better than no 2FA, and more than sufficient for the average person.
For someone looking to improve their security a bit more and for someone with a "don't trust anyone" model, having a separate 2FA app has it's advantages. It protects them against unencrypted password DB leaks, security vulnerabilities in the password manager, or any intentional security threat induced by the developer of the password manager
It is still a lot better than no 2FA, and more than sufficient for the average person.
For someone looking to improve their security a bit more and for someone with a "don't trust anyone" model, having a separate 2FA app has it's advantages. It protects them against unencrypted password DB leaks, security vulnerabilities in the password manager, or any intentional security threat induced by the developer of the password manager