The code provided is similar, but we've modified it heavily to work a bit better and with the standard login page. It works with Google Authenticator, so I assume other apps will be fine too.
I do agree with you however that two-factor integrated into Core would be very nice. I considered abandoning the work I'd done on these plugins to head down that path - that may yet happen - but have persevered with the code we have and modified it to bring it up to scratch. As such I'm running into some minor issues with the plugin approach for this.
Our use case is slightly different however as we're only allowing high level system context roles to use it - and to enable it they will be trained individually prior to enabling it for each user. I do see value in a user being able to enable it for their account however.
I've added into the plugin the ability to fall back and check all other installed auth plugins for authentication as the way it's provided it only works with manual accounts. We require this to work with LDAP/AD accounts.
I'm close to having a version of this available for testing - but I will need to complete my own testing first. I'm hoping to have something available to look at in a week or two.