while webroot method doesn't touch existing web server, the software dependencies for the letsencrypt client DO require root access to install i.e. yum or apt packages like python etc
indeed i agree, although never came across this with letsencrypt as I always ran as root user in the first place as I knew those software dependencies and web server do require root access to play with.
i use letsencrypt via webroot authentication plugin Letsencrypt Webroot Authentication Tested on Beta invited/whitelisted domain and Using the webroot domain verification method
my current LE integration progress https://community.centminmod.com/posts/20305/