It took a little bit for me to figure out Yukari's role, but I think it was that while Alice loved Marisa but was too dishonest with herself to admit it, Marisa was aware of it. So she asked Yukari to basically be a final boss so Alice could feel she earned the "goal", which is to say Marisa herself. So set up kind of like one of the games, so Alice would be more comfortable opening up in the end.
Not sure if I'm right, though.