Wait, are we talking about the same 2FA? I meant logging in with password and then 2FA with something like Google Authenticator from another device (mobile phone). If the password manager would do both of it, where would be the extra security?
I have seen folks use password managers to store their poor non-autogenerated passwords.
For users that do use the PW manager properly, having the PW manager store the TOTP secrets is indeed "putting all of your eggs in one basket".