Found Workaround! Seems OK So Far! But Is It Really?
After trying several different things through the ISPConfig 3 SSL Tab, adding in some SSL file uploads, and pouring myself a glass full of Tequila I finally found something that worked:
1.) Use ISPConfig 3 SSL Tab to create a self signed SSL cert for domain.com
2.) Make a backup of the files domain.key, domain.csr and domain.crt in /var/www/clients/clientX/webX/ssl
3.) Rename certified SSL files domainalias.key, domainalias.csr and domainalias.crt to domain.key, domain.csr and domain.crt and then upload them, along with the Root Cert and Intermediate Cert, to /var/www/clients/clientX/webX/ssl
4.) Then restart Apache: httpd service restart
This seems like the best way to do it because if ISPConfig 3 make changes to the vhost file then the SSL pointers in there will still match the certified SSL files.
If anyone has a better way please let me know. Hope this helps someone out!