2-step verification breaks continuity

After enabling two-step verification, Yosemite no longer correctly offers continuity features with my iPhone.

On my mac, I receive warnings from the FaceTime when I turn on "iPhone Cellular Calls" that I must log in to the same apple id with FaceTime and Messages. However, I am using the same apple id for both and even the same two-step app specific password.

How can I turn on continuity features when FaceTime is incorrectly warning that I am using different accounts on my Mac?