I presume you have the pass phrase enabled instead? It seems likely that only those with neither the pass phrase nor 2FA enabled are being nagged about 2FA after logging in with their username and password.
The solution seems likely to be to setup a pass phrase instead, but I've not tested.
"I already have a Passphrase - do I need 2FA as well?
The existing Passphrase system already provides an additional layer of security when logging into Online Services. 2FA is a more secure system because it requires the use of an additional device The Passphrase system will still exist if you would like to keep using it but if you opt to set up 2FA, the 2FA system and login will replace your existing Passphrase log in."
For those wanting to use 2FA, which uses Google Authenticator, perform a Google search for "Google Authenticator without mobile phone". It's possible to use GAuth with chrome and a desktop browser to generate the one time code.