Yep, and "using a password manager with a randomly generated password for each site" already mitigates that just as well.
Barring a user using 1Password and still reusing the same password on every site (why are you using 1Password then?) the only use-case I can think of for storing TOTP tokens alongside your password in 1Password is "the service requires me to use TOTP and I don't care about security".
That said, full disclosure, I've kinda got a bone to pick here because I was a long time 1Password user that was forced to switch off when 1Password removed the ability to have multiple vaults because, as they have said on their support forums, "It's called 1Password and our users only want one password." which was a... mind-boggling response from a company that should be focused on security. And this blog post really doesn't instill much more confidence than that response did.
These days I have my passwords in a KeePassX database. I have my TOTP secrets stored in two places--on my phone in an authenticator app where they're on a very secure platform and practically unrecoverable, and in an entirely separate KeePassX database that has nothing in common with my password database. The only time the KeePassX TOTP database is opened is when I set up a new service and want to add my TOTP secret. It's only there to "break glass in case of emergency" and allow me to recover access if my phone were to become unavailable. It's the right balance of risk _for me_, and in most practical sense two _factor_ authentication.