For example, my site (justbeamit.com), runs on GAE, but the naked domain simply redirects to the www.
AWS gets away with this afaik with some magic to point to the IP address for the loadbalancer that would serve your content.
Techincally you can find the IP address for your GAE subdomain and add an A record for your apex domain, but keep in mind that this is a bad idea.
For example, my site (justbeamit.com), runs on GAE, but the naked domain simply redirects to the www.