I'm Completely Lost

[pfg]

The biggest issue with that is probably that it’s usually not PHP “doing the SSLing”, but a separate web server like apache or nginx. While a Let’s Encrypt client written in PHP would work just fine, you will need to find a way to pass those certificates to your web server and force a reload. That’s usually not something you can do with shared hosting, where, if they offer SSL with custom certificates at all, it’s usually some kind of web interface where you have to manually upload the certificate. At that point you might as well use manual mode from your own PC, and upload the challenge files by some other means.