If your password manager has control of both your password and your "2nd" factor auth, it defeats the purpose of it being a 2nd factor.
You are still protected from your password hash being stolen from the target website, decrypted and then used for log-in, but if password hashes were accessed, potentially a bunch of other stuff that you'd care about is too, so that's a somewhat moot point.
But someone stealing your laptop and getting access to your password manager gets access to your 2FA too. Making it not a "second" anything: it's akin to using two passwords for log in to a single site and keeping them in the same place. Physical separation of the two authentication factors, thus, matters.
That also means that you should not have your password manager on the phone, or at least only have a separate one: ideally, password managers would integrate between desktops and mobile devices to pass short-lived access to passwords for Oauth/OpenID Connect auth instead.
Yeah, bridging convenience and security is a long standing nightmare of a problem to solve. :)