In Route C he does tell his pod that his goal is the extermination of all machine lifeforms. That is a clear and calm declaration of genocidal intent. The points you make, he has even more reason to not be racist than 2B does, yet he still clings to that hatred irregardless of what is reasonable. Even in the desert 2B has doubts about whether or not machines truly are as unfeeling as she's been told: 9S doesn't despite his hacking telling him that he's clearly wrong. He knows more than 2B and understands less than 2B because of his hatred of machines. As for him opening up to Pascal as you put it, he's still very dismissive of the idea that machines and androids can live in peace, which means he does still see Pascal as an enemy. Those quests are exclusive to him because they all involve hacking, that is they require a gameplay mechanic that is unique to him- that exclusivity thus tells us nothing. But again, when he comes to after 2B's death and calmly tells his pod that his goal now is to kill A2 and then kill every machine life form that is a clear declaration of genocidal intent. His actions after that are very much compatible with those stated goals: you say he targets N2, at this point he doesn't know about N2, he just happens to find out about that while he's on his way to kill as many machines as he can.