I've been using Let's Encrypt for a month now and I'm very happy. It's so easy to use and I don't even use control panels for my servers.
I was debating standard install of a cert generated elsewhere or sucking it up and installing Lets Encrypt and was thinking the install would be better longterm (on a VPS with several sites). And then out of curiousity I went to Manage SSL Certificates in Virtualmin for the site in question and was surprised to see the Let's Encrypt link. Five minutes later, the site was humming along on https:
>>CPanel
I assume that is not a choice you can make. In any case, once made, you pretty much have to burn a server down to get off CPanel because it gets in everywhere.
I recommend giving Webmin/Virtualmin a look if you have a chance. I think I would describe it somewhat like the difference between Windows and a Linux desktop GUI. CPanel takes over at a basic level (for many years you couldn't run git safely on a CPanel server, though you would think there would be no relation between the two). Webmin is more like a graphical layer over the command line.