Possible Fix: pull request, which in currently in review. Hopefully it will be merged and backported to earlier versions of the engine.
(Temporary) Workaround: currently the Rogulike 2D Kit requires a RoomPair (structure), consisting of a SetupRoom and PlayRoom Tile Map, for each playable room. The PlayRooms are duplicates of the matching SetupRooms, but have all the layers that should be ‘Hidden in Game’ removed.
I suggest creating all the SetupRooms first and when complete, duplicating the SetupRooms to PlayRooms and removing the obsolete layers. After that add the matching RoomPairs to the BP_TileMapRoom for play your rooms.