Saw it twice this weekend. It's a much different experience when you see it already having an idea of what it's about. The emotional impact is lessened, and you catch many more symbols and themes.
As Aronofsky said, this movie represents our Mother: the one who gave us all life, yet whom we neglect. Basically, J-Law is a Gaia-like figure. She builds and gives and loves, but is taken advantage of and utterly consumed.
The biblical allegory is just structural, not the entire point of the movie. It provides a reference for us to look at our progress as a species. The first half of the movie is the story of creation and the coming of sin to the world, ending with the biblical flood (the sink bursting). The creature J-Law flushed down the toilet is foreshadowing the flood, and I think symbolizes imperfect creation, or humanity. It's being flushed away, and a new version will be created to replace it.
The second half of the movie is basically all of human history taking place in the house. People band together, form tribes. They do primitive dances and worship. They share, eat together, and live together under God/Javier. Soon, they take. And take, and take, and take. Their sins become more and more egregious. God believes Mother's work (the house) is there to be shared, but Mother ain't happy about it. Soon, humanity sins more and more, escalating to murder. There is slavery, violence, zealotry and extremism. There is war and plague. I kept an eye out for famine and death, to represent all four horsemen of the apocalypse, but couldn't find them.
Then, the baby is born, representing Christ. He exists to redeem humanity and forgive them of their sins. But, humanity all wants a piece of Christ, and it is the last thing they take from Mother. Like the sacrament, the body of Christ is eaten. They want to be a part of it. They want to do whatever they can to feel closer to God. They even speak his words when eating Christ. Finally, they abuse the shit out of Mother, until she's had enough and destroys her home and its invaders in a fiery apocalypse. God is like "whoops, that didn't go well," and tries again all over. He's narcissistic and unable to learn and mature.
I welcome any further discussion of this movie. It's not perfect, but its most valuable asset is the way it allows people to talk about it.