Yeah those pedestral are for the skulls. Unfortunately both cables are hidden in the Asylum so you would have to restart the whole thing. You really have all 3 skulls? If so you did an awesome job i know they are pretty difficult to get.
The bad ending with the elevator is the one considered canon. Dismantled 2 demo will show more of this.
The hatch you opened is the one that you go through to go down the ladder and continue the game. This is not related to a secret.