It happens in nature too. Your skull has fewer bones in it than the skulls of many fish and humans do not by any stretch have the largest genome in nature.
The optic nerve connects to the front of your retina giving you a blind spot, then pokes a hole in the retina to get out to the back and off to the visual cortex which is at the other end of the brain. Intelligent design would do better.
[1] https://forum.donanimhaber.com/store/c9/ef/2d/c9ef2d955e3f99...
Currently we're constantly expanding the complexity of our systems, but since they don't understand their underlying purpose, they can't help us manage that complexity without drastically limiting their flexibility, there's no working around that.
But if they knew what they were doing, instead of "I need to reorganise this database stack to reduce overhead" we'll be giving simple commands like "please stop taking over the world" and letting the machines handle the complex details.