I went through the perfect setup on Ubuntu Bionic Beaver without any issues (I think), but the SSL on the ISPConfig control panel doesn't seem to work. I get the security warnings. Any idea what I could have done wrong?
This is no indication that's something is wrong. It just tells you that you are using an SSL cert that you issued yourself (self-signed SSL certificate), so as long as you trust yourself, that's perfectly fine. Btw. the encryption of a self-signed SSL cert is exactly the same than the one of an officially signed cert. Nothing, self-signed certs are used by default. If you want to use a SSL cert from let#s encrypt instead, see here: https://www.howtoforge.com/tutorial/securing-ispconfig-3-with-a-free-lets-encrypt-ssl-certificate/