She's the girl genius, she knows exactly what she's doing. That doesn't stop it working on her, it only means she gets as angry as it makes her sad, terrified. This is one definition of evil, this compassionate specificity: "I can only imagine what it must have been like for her, trapped up there all alone, watching the flames climb the walls, melting all the little glow-in-the-dark stars that she glued to the ceiling. Trapped in a box of living fl..." He burns himself, accidentally, with a match, and she jerks. Zoë rolls her eyes, and breathes, but it's too late: He knows. He's proud of himself, for breaking her.
I think the cheap VIP Room set has replaced the cathedral for that set's purposes. Have some extras walk by the black windows every now and then, thumping bass behind, and a random set of laser-show projections, and you're in the middle of a club. And given that Zoë isn't really God anymore, we don't really need the cathedral anyway. I did love it, though. So they're in there discussing how creepy Daniel was being, all the "soldier stuff" the robot already knows how to do. "And then he started barking orders at me like some crazy drill sergeant from one of those Tauron war movies." Lacy doesn't get it, and explaining it to her allows Zoë to put it together: The test wasn't the drills, it was the story. It was the way she wanted to kill him -- "reach out and snap him" -- for doing it.
"Zoë, are you still sure that it would be the worst thing if you did, you know, come out to him?" Zoë reminds her -- she was there when it happened -- how bad it got, when he wrapped his arms around her and put her in a cold, dark place. "If he really thought of me as his daughter, he would've never have done the things that he did." And ultimately, as chilling as that sentence is, she takes it to the obvious level, which is that she has only ever thought her father cared about his business, his science. His money, his work.
And where that takes us is fruitful, if well-trod territory. Zoë can't have her Daddy, so she hates and infiltrates his science, becomes a girl genius. Attempts to use the hard and software that he uses to transcend itself: To create something from her own forehead that will take down the whole sick world he invented. Zoë can't have her Daddy, so she hates and infiltrates his territory, eschewing and spitting on her mother's life, hiding herself even before she died, inside the tower. The things she wanted were the things she hated, and those are the things she tried to become, in order to evolve them past her mother and father both. Destroy the Matrix by making it a Heaven. Destroy the culture of Caprica, for celebrating Bill & Melinda above all others. Destroy science, and technology, and medicine, for being loved more than she was.