I’m afraid I don’t understand - could you explain further? Changing the domain of the site shouldn’t involve migrating via the Native XML import. You should just associate your new domain name with your site (how to do this will vary depending on the host you’re using)?
Sorry - not sure what to suggest here. I don’t see how this issue would be remedied by moving from away from a subdomain - lots of journals use a subdomain and have no issues with Google Scholar. Also - I can see that some of your journals are getting picked up by Google Scholar: Google Scholar -