where and how did you find that the ORN Emperor is actually Khaos?
I know you said that no explanations were given (unfortunately), but still, I don't think it is Khaos. It might be a bio-computer that was made during the beginning of the space age, but it was destroyed in TF V with Cenes and the Judgement Sword...
Just need some clear information as you have more knowledge than I do about Thunder Force.
I wanna ask : about the last stage (rather, the final boss Khaos Ascendant), shouldn't its name be Judgement Sword's route exit? Because it seems the appropriate place as it's the only access route to enter and exit the Judgement Sword.