The corrupt Lord Ambrose D'Arcy steals the life's work of the poor musical Professor Petry. In an attempt to stop the printing of music with D'Arcy's name on it, Petry breaks into the printing office and accidentally starts a fire, leaving him severely disfigured. Years later, Petry returns to terrorize a London opera house that is about to perform one of his stolen operas.
While they aren't in a domestic partnership, a character repeatedly hits another character, makes her work until she passes out, splashes sewer water on her face, and tells her that she can only work for him.
I'm not sure who the "yes" comment is referring to. Assuming it's the phantom, the phantom lived many years in a house before moving to the sewer cave.
In a colloquial sense. For example, Erik tells Christine to sing with "the beautiful gift God gave her." Additionally, the opera put on by the cast is about the life story of Saint Joan of Arc.
It's a gothic horror, so it's more bittersweet than anything. Every main character got to accomplish their goals and find happiness (even though one of the main characters die immediately after that).