Umm why wouldn't they? Or make and use any other skin like that.
Okay, sure, it would only affect them. Here's a scenario. You spot a normal looking P39Q. Knowing its rear view is obstructed you move in behind and below him slowly creeping up on him. Thinking to yourself you're about to get an easy kill because there is no way he'll see you.
Thing is he made himself a custom skin that only he can see. He looks behind him and instead of his view being obstructed like any other P39 he sees this.
He then sees you sneaking up, turns around, and kills you. You find out he is using an invisible skin, how do you react?