1. Those were androids (not replicants) based on the same models as Devola and Popola, NPCs from NieR. Essentially they drive the main quest. There is, however, a twist later that they have been trying to dissuade you from your quest all along because, as it turns out, you, the player, are not human, but a replicant. A replicant is an artificial body meant to house the soul of a human, but those bodies became sentient and think of themselves as people. The real people are turning into monsters because they could not reunite with their intended artificial replicant bodies. In NieR you doom mankind and replicants to certain death because you destroy the means of this gestalt/replicant merging process, and thus all real humans (in the form of souls) die. This directly means that all humanity is doomed and long dead during Automata. Anyway, the androids in Automata hate the Devola/Popola series of models because they think those two betrayed mankind (which they didn't really; they merely failed to execute their mission, which would have doomed the replicants but saved the actual humans, or what was left of them)
You may recall the scene in Automata where you attack that tower and it looks like you are about to fight the two red heads. This is a reference to NieR: if you played the game, at that point, you expect them to betray you and attack you, but the game subverts this and has them help you, making a point that you, the player, also bought into the prejudices the other androids had towards those two.
2. I do think there is an implied but never mentioned secret council somewhere whose sole job it is to keep the cycle of android/machine war going for eternity. This council may or may not be the pods. My theory is that some androids - now long dead - figured out that androids need a reason to live, and tasked the pods with keeping this eternal war cycle going.
3. Kaine is an important character in NieR which you save by deleting your savegame in that game. She is, of course, doomed to die, like everyone else except for Emil. Kaine has a very long and complicated story best experienced by playing the game. Great character. Project Gestalt... When Drakengard ended, the world was infected with something called white chlorination syndrome, a disease that wiped out humanity. A plan to save them was devised: split the soul away from the body and keep artificial bodies ready, to be inhabited by those souls once the world is no longer infected by that syndrome. Devola and Popola are two android designed by humans to oversee that process and the eventual reuniting of body and soul.