If you somehow got a LE certificate (with a method I'm trying to find out in this thread) you can copy and paste the whole certificate (not only the file hashes) in your web interface for managing this.
Just note that there is a separate thread tracking direct cPanel integration:
Because one thing is still missing in this approach: You have to renew the certs, so either you have to do this step every 90 days or you can automate it e.g. by using another method.