that is why 2p words and the stuff happening in the raid don't make sense,the catch is their original will 9s manipulates them against it.
once that sentence is out of the raid wibe and you see the wording ,it is clear that their original will isn't what we believe to be.
if this is like nier automata then the original will is probably to destroy the humans as their makers dictated.
if we follow nier then the machines from there who are identical to adam and eve means that they wanted to learn and know about humans. they were fascinated and curious about humans and our nature,in fact ,they even killed their own creators cause of that . they evolved beyond what their creators wanted them to be and in the end defy them.
and if this is the case,then the 9s who controls and manipulates the machines is 9s from ending D then the clue is in the final moment of the ending where he speaks about traveling and being calm and have no resentment like i thought then he might be "manipulating and controlling " the machines to not harm anyone and live like yohra and the humans.
we believe those notes in the quests belong to the machines of current time but what if it is before 9s time.it could be records from the time before 9s manipulated them or even before that it could be from the time their creators were alive.
even if it is related to ending D or related to ending A ,the fact that 9s manipulates the machines against their will is probably because the machines would have done something that will kill/hurt and interrupt humans lives.