There is documentation that provides guidance in regards to your question. Please see the following:
Adding SSL certificates to FortiClient EMS for Chromebook endpoints
Have you been through this documentation yet? If so, what are the "significant issues with the SSL certificate" are you encountering?
To answer your question, I am using a FQDN that I generated with my internal CA (so it required me to push the CA certificate through the google console to all of my chromebook hosts).