We're already using a map layer anyway for this - we have an "item" layer, and one of our many items is "spawn droid g101". At map load we scan the map item layer for tiles and process them. So we not only create droids, we're also creating turrets, lights, doors, and terminals. It's a very handy mechanism because what's going to be spawned can be represented in the map editor as a tile and so you can see what it's all laid out like and edit it in exactly the same way as you edit any other tile.
That brings up a good point. It is a good idea to visually represent those objects as extra layers in a tile map editor, assuming you only have at most one object of each type per grid location or can support different sized grids if you need to. If you have a good tile map editor already, then it's less work to treat it as a tile in a tile editor. If much less than one third of your grid is filled with enemies or other objects, then I would still use a "list" of tiles and not a "2D array" of tiles for those layers in my file format, even if not in my map editor UI.