CNAME is absolutely an issue, especially when using managed hosting. Many hosts require that you CNAME since they move around IPs. (e.g. Heroku) so unless you put a provider in front of them that integrates with your DNS you need www.
Disclaimer I work on App Engine.
Search in that same document for "naked domain".
> I'd like to map my app to a naked domain (such as http://example.com).
vs.
> App Engine does not currently provide a way to map static IP addresses to an application
the latter is that you own an IP and want to map it against your appengine.
the former is example.com -> appengine site.
(not related to google)
So you traded an intermittent problem (only relevant when an IP change occurs) for 24/7 guaranteed service outages for a (probably very) low percentage of your intended demographic.
Because I'm pretty sure we all know what I meant when I pointed out using Cloudflare means gaining a convenience at the expense of being at the mercy of third party outages.