Though we haven't tested this extensively there shouldn't be a problem with instancing RailClone objects so that you can control them all at once. The only caveat is that if you do use them in a boolean object, "Use Instancing Engine" is automatically disabled not just for the object used in the boolean, but for all the instances too. Check out the attached file for an example. All the instances are driven by a single spline but if you render it, instances are shown in green and static geometry shown in red.
I hope that helps.