Rape is in a different category from those other crimes. So is child abuse and torture. The perpetrators of these crimes need for their victim's lives to have value so they can enjoy destroying that value. The victims are weak, vulnerable, innocent and the perpetrator needs them that way for the crime to satisfy them.

The cops in GTA are neither innocent nor weak nor vulnerable. When you hurt civilians their pain isn't the point, they just happened to be in the way of your quest marker. It's not about cruelty.

Imagine if someone made a game where you just rape and kill kids and torture animals. Would that seem equivalent to GTA or would it seem like some fucked up serial killer shit?

Rape is by it's very nature an intensely personal crime. It is not possible to show rape without focusing closely, intensely and for an extended period of time, on the pain of that one specific victim.

It's not remotely in the same category as a random murder spree of NPCs, which is a more detached and unpersonal crime. Unlike rape, running around town and randomly using weapons of mass destruction to murder every civilian you come across, or single handedly invading a millitary base is so over the top and detached from reality that it detaches the acts from any real world connotation, and keeps them clearly in the realm of video games. Rape is, unfortunately, not detached from reality, and generally not that over the top or unrealistic.