Is this really the version you are looking for? Kentico 9 documentation is no longer updated. Use the switch in the header to choose your Kentico version.

Settings - Authentication

The multi-factor authentication settings have global effect. They cannot be configured for individual sites.

Multi-factor authentication
Enable multi-factor authenticationIndicates, if multi-factor authentication is enabled. Users can choose to enable multi-factor authentication when they register to your website.
Display initialization token

Displays an initialization token when a user tries to sign in to Kentico with multi-factor authentication for the first time. The user types the token into the Kentico Passcode generator mobile application.

Disable if you want to use customized multi-factor authentication (without the mobile application).

Multi-factor authentication is required globallyIndicates if all users in the system including newly created users are required to use multi-factor authentication.