It's personal preference. Do you want the HTML files (and other supporting website files) to be in a separate directory or right next the Rmd files? I personally prefer to keep the HTML files in a separate directory so that it is less cluttered.
One potential use case where the decision matters is hosting your website with GitHub Pages. There are multiple options for where to save your website files. If you choose gh-pages or master branch, then the HTML files need to be in the root of the project (output_dir: "."). If you choose the master branch docs/ folder, then the HTML files need to be in a subdirectory named docs/ (output_dir: "docs/").