I appreciate the case, but I do not find it compelling. The author makes no reference to the social tableau implied by any exchange of gratitude. "No problem" (or, more likely, "no prob") are a response to a casual "thanks." However, a casual "thanks" is generally more formal than whatever language we use regularly, so any "thank you" "you're welcome" assumes more monument than otherwise. We control two things by acknowledging gratitude: the tenor of our interactions in our immediate future with the grateful and the level of agreement as to the balance of indebtedness. If someone says "thanks so much I really appreciate it" and you answer "no prob" you're essentially stating that you do not wish further entanglements with that person. If you instead answer "you're very welcome" you're acknowledging that you did a big favor for that person and are comfortable that they would (will) reciprocate if the shoe were on the other foot. In casual discussions, amongst casual friends, dealing with casual favors, "no prob" is entirely appropriate. It fits the register.
Yes, it doesn't make sense to critique most idioms on the merit of their literal meaning. A phrase can mean whatever we agree it means. Certainly there are situations where an idiom may be rooted in, for example, racism, and in that case it's probably better to abandon it. But by and large, ascribing anything more than what we all accept a phrase to mean in context, is a waste of time.The author makes no reference to the social tableau implied by any exchange of gratitude.