Men having an affinity for certain types of video games is a symptom not an effect. The difference between the sexes in this area existed before video games were a thing.
The reality is that men have been observed to have, for whatever reason, higher proficiency at spatial reasoning than women long before video games were a thing. To say that 3d video games played by boys and men has led to boys and men being better at spatial reasoning is fallacious when it's known that this existed before video games were broadly available. It also is logical to see that video games that play into the strong suit of men and boys is going to attract more men and boys.