I'm using meta tags rather than HTML files to verify my site ownership, because I want to keep my root directory clean. In contrast, Google recommends the 'HTML file' method. My quick web search didn't return anything about the reason of this recommendation.
The verification method you choose depends on your web host. Use the HTML file method if you can upload HTML files to your domain’s web host. Use the meta tag method if you are unable to upload HTML files to your domain’s web host.
Here is a screenshot:
Is there any benefit (Google-specific or general) of the 'HTML file' method?