The junction controller does work for very short crossovers, and does not work reliably for long ones such as on a mainline where one junction will be released before the other. I used them extensively on my tram route to allow trams to crossover from a return loop and back on to the opposite main. They worked okay for that, but occasionally another AI train would come along and cause a derailment which left a tram and a half since I run double trams on my mainline.
More recently like pware, I have discovered the virtues of ITs. Using the EIT rule and setup, I've got four locations now that run automatically under the tower control. I will admit that this was one of the more difficult things I've ever done in Trainz, but it was well worth the effort. What I did find, however, is the paths need to be at least 2x the length of your longest train. In my case it's two connected trams. If the paths are too short, then there's a bit of a Mexican Hat standoff and the AI drivers go off and play Rock-Paper-Scissors indefinitely.