Yes, it only appears on the studio set.
Based on the design of the actual building, there wouldn't be room for the counter and the kitchen.
The real cafe has the counter on the back wall, and a mock-up effort on the wall where you would expect the kitchen to be.
What interests me is that I don't think we saw the cafe exterior in the pilot (you'll have to correct me if I'm wrong) yet the interior set and the scenery of outside is clearly based on the real building.