If you define a custom HTML policy then you are completely responsible for the HTML, including styling. Basically instead of Azure providing the default HTML it renders your HTML file instead. Inside your HTML you have to tell Azure where to inject its "sign in" elements. This gives you complete control over the formatting.
To inject something into the existing template while keeping its styling you should download the template that you want to use from Azure. The templates are available in the documentation link you provided. Download the template, add your custom HTML where you need it and store it in Azure. If you ever want to change the styling of the template (from say classic to blue), then you'll need to grab the new HTML and update it again.