I'm going to explain a few things, that might not have been very clear, but should help you understand a few events better:
In the last part of the game you go into the Hall of Echoes, the limbo-like world of Rivellonian mythology. In there you must find Ygerna's soul and to reach her you must battle some revengeful ghosts whom you have sent there. Afterwards you find her soul and undo Ygerna's death by stopping her execution in her memory. In her memory, mind you: this is not a reality in which you actually kill Zandalor and the Divine. Zandalor is still back in Aleroth. Then, when Ygerna is free, she betrays you and imprisons you in another dimension. This is not the Hall of Echoes! It is another place entirely used by Damian to incarcerate the Divine and now by Ygerna to trap you.
I think that explains some matters that you mention.
Nice work by the way, you have clearly given Divinity II a lot of thought.
