Interestingly enough, I think you missed one of the more important points by focusing only on the stop signs. Red lights can't be red lights to everyone in a lot of places simply by the nature of their construction. It's why the dead red laws exist, and it's that very often red lights were constructed with solely cars in mind and have sensors that cannot detect bikers that signal a request to the light for a change. While this isn't the case at all lights, it highlights the fact that there are clear differences in the classes of vehicles and that the control structures on the roads were designed with cars in mind, not bikes. These laws are simply attempts to rectify this in light of an increasing interest in bikes as a transportation method.