If I remember correctly, Datastore is basically a thin layer on top of Megastore[1] (aka the precursor to Spanner).
1: https://static.googleusercontent.com/media/research.google.c...
1: https://static.googleusercontent.com/media/research.google.c...
In this case Megastore provides the underly multi-region/datacenter K-V replication services.
All the database features like secondary & composite indexes, query language, multi-tenancy support, PAYG model, etc, etc, are built in the Cloud Datastore layer.
Interesting, so you don't use Megastore's indexes?