Any decent password manager would avoid autocompleting the password on the wrong domain in the first place. I.e.: it will already protect against phishing attacks anyway.
1Password's documentation use to have a whole article about how bad an idea it was to store TOTP in a password manager — but their stance completely changed at some point. Around the same time they started _recommending_ that you do so, and presented it as a key feature in the marketing material.
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Personally, I think that the only valid reason to store a TOTP secret in password manger is when you don't really care too much about an account (e.g.: prefer convenience over security), but the website demands that I set up 2FA.