I use Atlas O and I have never had an issue. I am currently building a new layout, but I have attached some pictures from my old layout I took down. If you ballast the track properly, then the tie height really is irrelevant. I also weathered the rails to look like rust and rail dust. I do plan on making some sort of removable cover that goes over the Atlas Switch Machines. Maybe hallow out some foam board and make it look like a slight hill that blends in with the ground. Something easy so I can still access the machine. Maybe this will help some folks out.
-Eric