Just got ending B and already 30 hours into the game, but I have a few questions.

I just got ending B over the weekend and have yet to begin route C probably this weekend, however I have a few questions about ending B. So aside from that top secret document, will I get more information about who created YorHa if the humans were already dead from Project Gestalt? Will it ever be explained why the androids lied about the humans still being alive, because if I am correct the whole purpose of the mission was to eliminate the machines and have the humans return to earth?
Don't go in depth with those questions because if it is explained in route C/D/E, then I want to find out for myself. I also have a few spoilers that I've gotten long before I got the game, and I want to ask if it's going to ruin the story of routes C/D/E, because I've heard people say that this is were the story actually begins and that routes A and B were just the "prologue", and I honestly don't get why they say it. Don't tell me why though! So, the spoilers. A2 has to erase Pascals mind. I don't know why this happens, but if you do it you get the Machine Heads weapon. I don't know if it leads to another ending that isn't C/D/E. There was a video that had the commanders eyes red on the thumbnail. The video title was by my memory "Nier Automata Commander Spoiler". I am really confuse as to why this happens, since in endings A and B I find out that 9S was infected by Eve's corrupted data but then he had that die along with his original body while talking about how he can't let this data into the bunker. Again, I don't know if this stuff happens, (and don't tell me if it does), but assuming that it does happen, will it ruin the rest of the story and the Nier Automata experience. Sorry if this post is too long, I am just a little curious. -_-