Even if the serving component runs on Google App Engine, you don't have to deploy or manage it yourself. Once you activate Cloud Datastore you can access it like an other Google APIs:
https://developers.google.com/datastore/docs/apis/v1beta2/
If you want to charge for instances then the way to do it is the DynamoDB’s way — charge for throughput. The actual number of instances should be an implementation detail. At least that way it’s deterministic and you can feature it prominently on your pricing page with an appropriate calculator.
Until then the advertising is completely misleading if not dishonest, since I’m pretty sure the instance costs would be quite significant for any use case that tries to use “Cloud Datastore” as a standalone db solution for GCE ecosystem, rather than to just run some Map Reduce for an App Engine app.