During my first attempt at installing the Office suite through O365, I began running into issues with the 'Invalid Security Certificate' warning popping up every few minutes after setting up the associates Outlook profile. This customer already had the proper GPO in place set to disable SCP look up, exclude httpautodiscoverdomain, etc, which had been effective at stopping this from occurring in the past with your standard Office install. After updating the ADMX files (which include a number of new Autodiscover policies) to the latest set in hopes of resolving the issue, the issue with the certificate warning continued to surface every few minutes. After doing some reading, I discovered there are two registry hives that can manage Autodiscover:
Computer\HKEY_CURRENT_USER\Software\Microsoft\Office\16.0\Outlook\Autodiscover
Computer\HKEY_CURRENT_USER\Software\Policies\Microsoft\office\16.0\outlook\autodiscover

The latter Policies hive is where the key changes take place when managing via GPO, which was not performing the intended way with this O365 setup. I manually tested adding the Excludehttpautodiscoverdomain key to the first hive, and the security warnings stopped immediately. I tested disabling and enabling keys in both hives, and was able to confirm the finding. I have not had an opportunity to see if this issue exists for any other workstation/customer, but hopefully someone might find this useful if they do. I wound up just adding this key in via the registry via GPO and had no further issues after it was applied.