DNS and Auto-discovery configuration is setup correctly for both domains, yet only the Primary Domain configuration is working correctly.
Is it possible to get each domain Autoconfig/Autodiscovery working correctly. Is there a definitive guide to setting up multiple domains in Axigen. If this is not possible I shall not be purchasing a license.
Yes, having multiple domains configured for Autoconfig / Autodiscover should work without problem.
Now, the missing bits may be if there have not been set the virtual hosts needed for domains that are not covered by the default certificate used on the WebMail HTTPS listener.
Hint: we have customers that have chosen to use single certificate that is covering all their hosted domains (not many in their case) via Subject Alternative Name (so using a single certificate for *.domain1.tld, *.domain2.tld, etc)
The main debugging technique is to open the targeted URL (like https://autodiscover.domain2.tld) into your preferred web browser and see if the SSL certificate is reported as valid.
My assumptions is that you have a star certificate for your primary domain on the WebMail HTTPS listener and all you have to do is to configure new virtual hosts and their SSL certs via WebAdmin > WebMail > Virtual Hosts > Add Virtual Host for needed hostnames (like autodiscover.domain2.tld or / and autoconfig.domain2.tld).
Pay attention to enable Use specific SSL configuration for this virtual host so the configured certificate will be selected automatically. More information about SNI could be found here).