Hi. The fact is that part of the settings are compiled inline in Head. These settings will work with different template styles on different pages. But why do you need an extra code in Head? It is bad for performance.
Another part of the settings is compiled from SCSS to template.css file. This file is the one for all template styles. Thus, it will only be the code of the template style that you saved the last.
As far as I understand, in HU 2.0 this problem will be solved. But not in the current HU.