In my game I have a separate tilemap and tileset for game logical tile.
StartPosition is tile with index = 0
Enemy1StartPosition is tile with index = 1
and so on...
With this code you can find the index and position:
var elements_tilemap = get_node("elements")
var elementscells = elements_tilemap.get_used_cells()
for cell in elementscells:
var cell_tile_id = elements_tilemap.get_cell(cell.x,cell.y)
var tmp_pos = elements_tilemap.map_to_world(cell)
You can add then the enemy scene to the position of Enemy1StartPosition.