This documentation is not using the current rendering mechanism and is probably outdated. The extension maintainer should switch to the new system. Details on how to use the rendering mechanism can be found here.
To enable the YubiKey two-factor authentication for a user, just edit the user in the TYPO3 backend and enable the checkbox as shown below.
Next you have to enter the YubiKey ID, which is the unique ID of the YubiKey USB key. To get the ID, just insert your YubiKey into a free USB port and press the button on the YubiKey. Now a YubiKey OTP will be inserted in the textfield. Don’t care, that the textfield will show the whole YubiKey OPT. The authentication process will automatically extract the YubiKey ID from the OTP.
If you have multiple YubiKey devices, you can save the YubiKey ID of each device in the textfield. Remember to use a new line for each YubiKey ID.