Dictionary.com is telling me that "chemistry" mean "the interaction of one personality with another", so maybe we just have different definitions of what the word means.I still think it's weird to call that "chemistry" though. Chemistry implies something on the part of the actors.
Like where they look so unnatural together, it doesn't matter how good the writing is, they just won't work.
That doesn't really make sense in anime, though, since actors are only using their voices and at least 90% of chemistry is body language. So you can easily have animators work around that if two voice actors don't have good "chemistry" together.
If you write 2 characters whose personalities don't mesh together, it doesn't really matter if the animation makes it work if the writing behind it doesn't. It all comes down to whether or not the writing makes it work or not. Good animation is just wasted if they're portraying a bunch of paper thin personalities.