> if the scripting media query was ubiquitous I would never go back to toggling classes via JS

I am asserting that in the majority of cases where a person's browser is not running a page's JavaScript, it is because of a network failure or intentional blocking, neither of which can be detected by the media query.

Therefore, three years from now when the media query will be ubiquitous, it won't prevent your styles that are meant to be used only with your JavaScript from being used most of the time.