Yes, there is sometimes an internal logic in the sense that it’s possible to find reasons for why language evolved in one way or another. (Historical linguistics is a field!) But that doesn’t have to follow any criteria that we might care about, like consistency or expressiveness.

To stretch your biology analogy even further: sort of like how humans have an appendix.

I wouldn’t try to read anything into culture based on the specific set of pronouns any language has. Turkish and (spoken) Chinese have never distinguished between “she” and “he” and it’s not because knowing someone’s sex is less important in their cultures than it is in Indo-European ones; it’s just random chance.