Hi, I think if you are able to ride the correct position on the tt bike and get enough aero benefit without losing power, the tt bike should win. On a truly flat course, the benefits of aerodynamics and efficient power transmission should outweigh the benefit of comfortable riding position and lighter weight.
I've found to my cost in the past that the point where a road set up becomes more efficient is much longer and more hilly than it feels like it should be.
Sometimes, on very technical twisty courses the road bike gets back some time even without hills, but that depends on the rider as well.
Peter