I figured it out! Rather than pre-creating the tilemaps inside of the prefab, You just have to add the tilemaps after the prefab was created (in the game).
You can add the 3 tilemaps to the grid in the awake function and use their variables:
GameObject go = new GameObject("Main");
mainTileMap = go.AddComponent<Tilemap>();
TilemapRenderer tileRenderer = go.AddComponent<TilemapRenderer>();
mainTileMap.tileAnchor = new Vector3(0, 0, 0);
tileRenderer.sortingLayerName = "Default";
and do this for every tilemap. The 'mainTileMap' GameObject will store the reference to the tilemap.