Hello Yihang,
The App Engine application incurs costs when running. Billing begins when an instance starts and ends fifteen minutes after a manual instance shuts down or fifteen minutes after a basic instance has finished processing its last request. You may find more detail on the "App Engine Pricing"
page. In other words, this mandatory app would not cost you, if your main application runs on a GCE instance.
Datastore usage costs are calculated in terms of stored data, entity reads, entity writes, entity deletes, and small operations. None of these involve the active App Engine application, if the only use you make of the Datastore is from your GCE instance.