Hello! Welcome to Flarum,
I'm not sure that I fully understand what you mean, but the header background is set to the exact primary color value (if colored header is turned in the admin panel of course), the line you are referring to defines the background color of elements such as buttons located in the header when the header is colored.
.define-header(true) {
@header-bg: @primary-color;
@header-color: @body-bg;
@header-control-bg: mix(#000, @header-bg, 10%);
@header-control-color: mix(@body-bg, @header-bg, 60%);
}
Could you explain a bit more perhaps ? I am most likely missing what you mean.