Advanced Themes allows you to add content into your theme without having to clone the theme. There are a few advantages to doing changes this away.
When updates come out for things that make the site responsive if you are using a default theme the updates would be made automatically. If you have a cloned theme then it might be harder for those updates to get installed as it might break the site.
- Custom Headers - META data would be an example of code that could be placed here.
- Custom Scripts - Java Script would be an example of data that you could add in here. For instance, if you were adding a slider to your site the Java script code could be placed here.