Re: Why root over directory?
Not sure if this is why the instructions suggest as much but there are search optimization considerations
Each subdirectory in your architecture is a level of less importance in the eyes of a search engine. Putting everything below root.com/blog/post tells the engines that post is less important than /blog/ which is less important than root.com
subdomain.root.com adds more weight to the relevance of a page to keywords.
subdomain comes with its own unique challenge of being considered a distinct site from root.com or othersubdomain.root.com. That can work for you and against you depending on how you structure the site overall and how you link within the site to each section.