Agree with Josh. Another thing it sometimes does is route you out of your way to put you on bike paths, sometimes for short distances.
One time out of curiosity, I asked for directions between two points on the Trans Am route. Can't remember the starting point (maybe, Wisdom, Dillon or Twin Bridges), but the end was W. Yellowstone. The rotue was remarkably different than the ACA route. As Josh describes, it chose a remote route with many miles of unpaved roads and very few (if any) services). I suspect that's because it's not considering the needs of the self-contained cyclist. That type of route is fine as long as you know what you are getting into and can prepare properly with things like sufficent water and nourishment. But if that's not your thing, you have to scrutinize the chosen route with care.