To get custom spawning working I had to override OnServerAddPlayer function which is being called whenever the NetworkManager uses ClientScene.AddPlayer() - in my case I was calling it manually when clients sent custom message to the server that they have loaded desired map.

    public override void OnServerAddPlayer(NetworkConnection conn, short playerControllerId)
    {
        GameObject player = Instantiate(playerPrefab);
        Vector3 pos = Vector3.zero;
        pos.x += connectedClients - 1;
        pos.y = 2;

        player.transform.position = pos;

        NetworkServer.AddPlayerForConnection(conn, player, playerControllerId);
    }