Yep, the SSL interface is confusing (like, why do you have to verify the subdomain when you already verified the root domain? In what universe do you have control of the root domain but don't control the subdomain?).
Anyway, when adding the domain to appengine, at the second step you *can* remove the www one (I've done this Monday actually). So the workflow is something like:
- go to the setup page
https://console.cloud.google.com/appengine/settings/domains?project=<your project>
- click "Add custom domain"
- select "Verify new domain" from the dropdown
- after completing verification in the webmaster tools, click the refresh button
- now it will display two text boxes (as you've said) one with "
www.foo.com" and one with "
foo.com" but you can use the X on "
www.foo.com" (on the right end) to remove it and leave only "
foo.com" (or the other way around).
Ie. you don't have to add both domains suggested by Google.
And a good point about having to be the verified of the domain in Webmaster tools.
Cheers,
Attila