Him - God, create, from ashes a brand new world to live in. Then he invite in Men and Women.
Their presence is infuriating to mother and result in bringing two brothers (Cain and Abel). Murder of one them result in even more people coming to the house and even more frustrate mother.
Him, creating new poems is the equivalent of God writing Bible. This spawns even more fans coming to the house, destroying it in the process. Military trying to help Mother are laws and reason failing when confronted with cult and fanatics.
Mother gives birth to all the things that are on the earth. Him, giving it to humans without mother consent and knowledge is God saying:
I give you every seed-bearing plant on the face of the whole earth and every tree that has fruit with seed in it. They will be yours for food. And to all the beasts of the earth and all the birds in the sky and all the creatures that move along the ground—everything that has the breath of life in it—I give every green plant for food
Fans killing it and then devouring is the humanity that slowly destroy each things that is on the planet.
Mother lighting the oil tank is the nature destroying earth as result, and punishment for humans actions.
Him, being intact in the whole process shows that God will repeat the whole process over and over and he don't care about people or mother. And the sixth day ends.
And for your questions:
- Mother is everywhere because she is HOME. The Man is a guest, and unwelcome guest to begin with that don't know how to act as a guest.
- and 4. Illness is the flaw in humans. BUT the flaw is in Man not the Woman. The wound on the side is when God taken out Adam's rib to create woman.
- (should be 1.) God is the one that speaks in Bible. Nature/Earth is mute and seemingly passive. The whole movie is an allegory about how Man are dominating women and bringing her to passive, child birthing item that have no power in speaking about their lives, child that they born and what surround them. The publisher is the male that speaks in the name of women but take role in the process of destroying them.