If you want to customize the output of the generator, the best way to do so is with a custom post-processing logic. You’ll have to implement the Run method which will be called after a level is generated. This method receives an instance of the GeneratedLevel class on which you can call the GetSharedTilemaps() method to get all the tilemaps from the level. When you have the tilemaps, you can find the ones that need a different layer and change that layer.
Let me know if that helps.