HTML is considered minified when all of the html is left justified and there are no spaces or gaps between lines. To keep the output human readable, it is helpful to ensure there are line breaks between elements. Thus these are added if needed. This includes the HTML that is generated by the theme template. This is relatively easy to do when generating HTML output and is a good practice to implement. If this is done on a consistent basis, there should be no need for an HTML minification plugin to do any work after the fact, eliminating a step in the optimization process.