As long as 90% of businesses use it on their desktop it makes sense to teach. Using windows and the common software (photoshop, excel etc.) on it is basically a life skill at this point in time.
I agree with your premise though.
I guess it could be argued the computer proficiency skill is transferable (from Linux at school to Windows at work) as long as there is a significant overlap in the available software, desktop presentation, workflow and control conventions.
One example where it for sure doesn't work is gimp to photoshop. If you wanna know why, go dig out instructions for how to draw a circle in each one. Or try recreating one of the many effects from PS in GEGL. - The workflow is so fundamentally different that if you know one software, it will actually hinder you learning the other, because your intuition will mislead you and you'll be constantly frustrated (which actively hinders learning. There are studies on that)