While it's technically possible to have multiple hostname aliases in one virtual host configuration, that will introduce a URL canonicalisation problem. 301 redirect to the canonical hostname would be the proper response to those requests.
it's not your only option. for example you could serve content from example.com.au and serve nothing or a redirect from au.example.com. if you serve content from both, without specifying anything, your example.com.au urls will appear in the google.com.au index and the au.example.com urls will appear in the google.com and perhaps in some other country-specific indexes.