What you add to something should -- or more often, needs -- to play to the rules of the thing it's being added to, though. If the game you're adding the content to consistently provides some level of foreshadowing, connectedness, or whatever other form of lead-up to its events, then it's sensible that what you add to the game from elsewhere ought to do the same.
There will of course be some shock and awe figures that are only explained later, like Midgardsormr, some room for twists and the like. But simply throwing players into another franchise inconsistent with all that's come before it, sharing no references, patterns, or themes, is not setup for a twist. It's just a lack of effort that ignores the game surrounding it. That's not subversion; it's neglect.
I love NieR. I like that there's a crossover for it, even if I'd have preferred Yoko Taro work his magic on an actual XIV plotline, rather than merely borrowing the poster children of another franchise in place of coming up with something of our own. But the shallow means by which it's been attached to the game isn't even worth defending, imo. Fun enough raid, but an incredibly poor effort to connect it to XIV.