Heya,
I would suggest that you check out the documentation for web root related to let’s encrypt which can be seen here but i will quote this part:
The webroot plugin works by creating a temporary file for each of your
requested domains in ${webroot-path}/.well-known/acme-challenge.
Then the Let’s Encrypt validation server makes HTTP
requests to validate that the DNS for each requested domain resolves to the server running certbot.
Basically it doesn’t really matter for certbot where your actual webroot really resides as long it’s served under domain you’re trying to obtain certificates for. For example you can set the path for your web root to be var/www/html or it can even be randomfolder. I use personally /root path to store certificates for a group of servers.So it’s more of a personal reference.