In the meantime, I bought a year’s certificate from my GoDaddy reseller account for $30 and installed it. It was getting too cumbersome.
The reason I’ve been using the web interface, like with ZeroSSL, is because my server is very non-standard. While it uses Apache style cert formats, it’s not a standard web server running on Linux. It’s a special web server + object-oriented database server that’s stand-alone and runs on Linux, with users, forums, and other features. It has a built in HTTP server of it’s own.
So until we can update it to automatically use Let’s Encrypt (like I can with my WordPress accounts) I have to manually get cert updates and enter them into the control panel of this server.
That was very easy to do with ZeroSSL. And it’s easy to do when I buy a cert via GoDaddy.