Like its style.css has body
So am I supposed to keep the background transparent, so I always make a good html5 website?
Are these default ?
Should I override them as per my website ?
If you are starting to explore HTML5 and CSS3 then this is a fantastic starting point but you should always adapt (and ideally form your own boilerplate tailored to your sites and coding style) the core code as you learn and start to create HTML5 sites.
In the CSS, the code included is for a CSS reset, based on resets mentioned in the code comments. So where the body background is transparent this is to make sure it is the same in every browser. There is an empty section in the CSS for your own styles:
200. /* Primary Styles 201. Author: 202. */
So if you wanted a specific background colour you can state it here, along with any other styles you add.