Writing entities with the same ancestor (parent) entity DOES really guarantee consistency.
How?
You were wondering how this can be: "It seems that the parent entity would have the same issue as the children - That multiple instances could exist at different datastores."
The answer is that there is a very sophisticated algorithm (google for Megastore papers, and the PAXOS algorithm, if you are interested in the technical details) that implements ACID transactions on entity groups even if the entities are on different machines!
Why restrict ACID to entity groups?
You may be wondering then why they don't do this for the entire datastore. It seems like they figured out how to do ACID transactions on entities that are distributed, then why not implement it regardless of entity grouping?
The answer to that is that the ACID transactions comes at a cost, and the cost is this: You can only have up to 5 writes to an entity group per second (actually it is more like 5 write transactions per second, so you can batch write in the same transactions to get better write throughput). So if they did this for the whole database, it be practically useless for the internet scale they are aiming for.
Reading after writing gotcha:
As a side note, you have to be careful if you read an entity after it has been modified (within the same transaction). The semantics of datastore transactions are such that reads see the data as it appears at the start of the transaction. This means it won't see the writes that have occurred inside the transaction.
Recommending reading (well, viewing)
This is almost a required video to watch if you are using the datastore. It will clear up a lot of these issues for you: Google I/O 2011: More 9s Please: Under The Covers of the High Replication Datastore