Challenges with New Style Guide and Theme Management

So with the new style guide, when you switch themes, the button colors etc is not part of the themeing so in the old version, it made more sense because I could just ad in the classes needed and then when I added a class on top of a section with something like "theme-orange" everything would inherit, so background, text, buttons and some custom elements we reuse in every project would just "work" by applying one single class. In the new everything is divided up and then we have themes, so I added in our colors in folders etc, but then the whole idea of changing the look of a section kind of vanish, or am I just tired? Please advice or send me a tutorial on how it's ment to be used. Even just switching from dark to light etc brakes in the out-of-the box solution when it comes to black/white buttons etc so im prob thinking about this in the wrong way.