Mix into FF14 lore? No, and imo, it shouldn't. Nier has redonkulous lore both in scope and scale. I really wouldn't want to deal with the implications it would bring to 14. Having this incident be a more or less secluded one is ideal.

I am more or less certain the story will be fine, and impactful in some way on the Nier lore. I also expect more Nier-ish raid mechanics and red balls, which I like.

Something I hope for, but doubt we'll get is a crushing existential crisis, with a side dish of Yoko Taro flavoured depression. Guess I can keep hoping though.