Please consult RFC 5785
for the meaning of the .well-known URL prefix i.e. the use of a .well-known folder in web sites. This is used, among other things, to confirm the ownership of a domain name when using Let's Encrypt or Keybase.io.
We added it as a default option in Admin Tools 4.0 on purpose. Many hosts which use cPanel now offer a single-click SSL certificate installation through Let's Encrypt. That makes use of the .well-known directory to verify ownership of the domain. If access to the directory is disabled by default –as it was in previous versions of Admin Tools– obtaining an SSL certificate automatically was impossible. Since there is no security threat from allowing web access to the non-executable contents of that directory and there is a great security value in HTTPS being widely used on as many sites as possible we decided to whitelist this directory by default.