Evolution, which is a basic fact of science, completely destroys the most important hiding place for the god of the gaps. Evolution makes a god's magic wand unnecessary to explain the development of new species. A magical being (aka a god) with nothing to do is a magical being who doesn't exist.
Of course a superstitious person who was desperate to have a reason to believe in a magical being could always invoke its magical powers for some unsolved scientific problem, like for example how did the first simple living cells get a foothold on Earth almost four Billion years ago. But what's the point of hiding its magic wand there when eventually it's going to have to find some other hiding place.
Also, if a god fairy is not necessary to explain something as complex as the development of new species, it's ridiculous to pretend it might be necessary to explain something else.
The choice is reality (science) or fantasy (a god fairy's magical powers). Most educated people, especially the world's best scientists, have chosen reality.