You should use a reference atlas anyway. Pure reference atlas. The idea is that before deploying, you can clear the reference atlas's pointer, and do a build. Then when you actually run your scene, none of your atlases will be in memory until you explicitly choose one and Resources.Load it. With your approach you will have two atlases in memory at the same time, which is bad. Plus each atlas prefab has its own data, so that gets duplicated too... with the reference atlas, it's empty, so you don't get this.
All atlases need to have identical sprites. Instead of "Interstate-64" use "Interstate", for example -- something that doesn't have a number that changes between your atlases.
