App Engine automatically manages the instance life cycle. https://cloud.google.com/appengine/docs/standard/java/how-instances-are-managed#startup has more.
The major driver of cost on App Engine is Datastore Reads. If you have any traffic, you can absolutely incur costs without pushing any forms to it. See https://docs.opendatakit.org/aggregate-app-engine-legacy/#minimizing-fees for more information.
$900/month seems unusually high, but if you used the biggest machines, large forms, and use Briefcase hourly, then I suppose it's possible.
This opaque pricing is one of the reasons why are removing Google App Engine support. If you are setting up a new project, it might be easier to go with a Digital Ocean or Google Cloud where performance and pricing is predictable. Oh, and you probably know this, but Fusion Tables will shutdown in December.