Older crossing signals, like the Lionel 154, used a special contactor, the 154C, to produce a not-very-realistic flashing of the two red lights. (http://pictures.olsenstoy.com/cd/accs/acc154p1.pdf) This is not something that would be easy to duplicate with an insulated control rail.
Otherwise, you would need to have a signal that included the necessary electronics to do the flashing when turned on by a control rail, or to add those electronics to something like a 154. I and others have posted circuits for doing this.
Do you understand how a control rail works? It is just an insulated section of one outside rail. You wire the control rail and the common rail on the other side of the track, the accessory, and its power supply all in series. The power supply usually (but not necessarily) has a connection with the track common. If you can give describe your transformer and crossing signal, we can be more specific.