I am going to disagree with you, but only for one animal. The Dodo.
We know it existed. We have reference images and actual stuffed birds and bones to study. And unlike the dinosaurs, which it can be said that nature wiped out, it is not to much of a stretch to say that either (for the purposes of a game) that some still survive somewhere or a 'what-if' scenario along the lines of what if we never wiped them out and actually saved a few of them?
So yes, I agree, there are animals that shouldn't be in Planet Zoo .... but the Dodo isn't one of those animals.