I understood your problem. This is not a bug, but a natural limitation.
Helix has one template.css file, regardless of the number of template styles. This file is compiled from the latest saved settings. Therefore, if you need several template styles with different appearance you should use only CSS coding, but not settings. In each template style, in the layout tab, you can add unique classes to sections and use them in your code.
In my practice, I always use one template style. If I need another appearance on a separate page, I use a page class to create a unique appearance in CSS.
Settings should only be used if you use the only one template style.