Unless those difference are part of the "design". Which they clearly are.
There's a subtle argument against an intelligent designer in the fact that an intelligent designer need not have created life with all of thesenested hierarchies, but a godless universe with common descent will show us only one of these possibilities perforce. By itself, it isn't a particularly compelling argument, but with the other examples f the same thing occurring elsewhere, it is.
For example a universe created by a god might feature a god that can be known by the senses or not, but in a godless universe, such a belief could only be held by faith.
In a universe created by an omniscient, omnipotent god, there need be no physical laws or fixed physical constants, but a godless universe cannot function without them.
In a universe created by an omniscient, omnipotent god, the beasts might have been formed into a peaceable kingdom, with no suffering. In a godless universe, we don't expect to find that.
In a universe designed for us, we might hold a special place in it at its center, and with the earth possibly being the only planet. In a godless universe, we expect that we do not hold a special place in it.
In a universe with a loving, caring god, we might find no needless suffering. In a godless universe, we are not surprised to find suffering, even in the undeserving of it.
And so on. In every case, when a god could have done it otherwise, but a godless universe would have to be much more restricted, we find those restrictions.
This is called consilience - when multiple events that individually aren't that persuasive begin to accumulate, the argument becomes much more persuasive, like the tax cheat who makes 21 errors on his tax returns, each in his own favor. No one of them makes the case for tax fraud, but collectively, they do.
So yes, perhaps what you mentioned was designed. But why in the way that it would be in a godless universe? And why are so many other things as we would expect in a godless universe?